Spike protein S1
Severe acute respiratory syndrome coronavirus 2
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain R； UniProt 333–528 | Not recorded | BA.2-13 heavy chain × 1 BA.2-13 light chain × 1 Nanobody C1 × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 GOL GLYCEROL × 5 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BICINE pH 8.5, 15% PEG 1,500 | Resolution 2.74 Å R-free 0.258 |
| 2 | Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain X； UniProt 333–528 | Not recorded | BA.2-13 heavy chain × 1 BA.2-13 light chain × 1 Nanobody C1 × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 GOL GLYCEROL × 5 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BICINE pH 8.5, 15% PEG 1,500 | Resolution 2.74 Å R-free 0.258 |
| 3 | Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain Y； UniProt 333–528 | Not recorded | BA.2-13 heavy chain × 1 BA.2-13 light chain × 1 Nanobody C1 × 1 ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 GOL GLYCEROL × 4 PG4 TETRAETHYLENE GLYCOL × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BICINE pH 8.5, 15% PEG 1,500 | Resolution 2.74 Å R-free 0.258 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 8C3V | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 10MU SARS-CoV-2 S2 in complex with polyclonal Fab_Donor2 Deposited 2026-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
698–1161（464 aa）
Chain D
698–1161（464 aa）
Chain E
698–1161（464 aa）
|
Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 11HK SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (Fab local refinement) Deposited 2026-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
914–1131（218 aa）
Chain A
703–833（131 aa）
Chain D
914–1131（218 aa）
Chain D
703–833（131 aa）
Chain G
914–1131（218 aa）
Chain G
703–833（131 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 11HL SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to the VN01H1 Fab (S2 local refinement) Deposited 2026-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
914–1131（218 aa）
Chain A
703–833（131 aa）
Chain B
914–1131（218 aa）
Chain B
703–833（131 aa）
Chain C
914–1131（218 aa）
Chain C
703–833（131 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 11HN SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to C77G12 (S2 local refinement) Deposited 2026-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
914–1131（218 aa）
Chain A
703–833（131 aa）
Chain B
914–1131（218 aa）
Chain B
703–833（131 aa）
Chain C
914–1131（218 aa）
Chain C
703–833（131 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 11HW SARS-CoV-2 spike S2 trimer stabilized in the early fusion intermediate conformation (E-FICs-v3) bound to C77G12 (Fab local refinement) Deposited 2026-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
914–1131（218 aa）
Chain A
703–833（131 aa）
Chain B
914–1131（218 aa）
Chain B
703–833（131 aa）
Chain G
914–1131（218 aa）
Chain G
703–833（131 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 6LVN Structure of the 2019-nCoV HR2 Domain Deposited 2020-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1168–1203（36 aa）
Fragment：HR2 domain
Chain B
1168–1203（36 aa）
Fragment：HR2 domain
Chain C
1168–1203（36 aa）
Fragment：HR2 domain
Chain D
1168–1203（36 aa）
Fragment：HR2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Tris HCl, pH 8.5, 25% PEG3350
|
Resolution 2.47 Å R-free 0.258 |
| 6LXT Structure of post fusion core of 2019-nCoV S2 subunit Deposited 2020-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
910–988（79 aa）
Fragment：HR1 domain,HR2 domain
Chain A
1162–1206（45 aa）
Fragment：HR1 domain,HR2 domain
Chain B
910–988（79 aa）
Fragment：HR1 domain,HR2 domain
Chain B
1162–1206（45 aa）
Fragment：HR1 domain,HR2 domain
Chain C
910–988（79 aa）
Fragment：HR1 domain,HR2 domain
Chain C
1162–1206（45 aa）
Fragment：HR1 domain,HR2 domain
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 2 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；10% PEG 8000, 200 mM zinc acetate, 0.1 M MES, pH 6.0
|
Resolution 2.90 Å R-free 0.290 |
| 6LXT Structure of post fusion core of 2019-nCoV S2 subunit Deposited 2020-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain D
910–988（79 aa）
Fragment：HR1 domain,HR2 domain
Chain D
1162–1206（45 aa）
Fragment：HR1 domain,HR2 domain
Chain E
910–988（79 aa）
Fragment：HR1 domain,HR2 domain
Chain E
1162–1206（45 aa）
Fragment：HR1 domain,HR2 domain
Chain F
910–988（79 aa）
Fragment：HR1 domain,HR2 domain
Chain F
1162–1206（45 aa）
Fragment：HR1 domain,HR2 domain
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；10% PEG 8000, 200 mM zinc acetate, 0.1 M MES, pH 6.0
|
Resolution 2.90 Å R-free 0.290 |
| 6LZG Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2 Deposited 2020-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–527（209 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES pH 6.5,10%w/v PEG 5000 MME,12% v/v 1-propanol
|
Resolution 2.50 Å R-free 0.216 |
| 6M0J Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 Deposited 2020-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–541（223 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.1M MES, PEG5000mme
|
Resolution 2.45 Å R-free 0.227 |
| 6M17 The 2019-nCoV RBD/ACE2-B0AT1 complex Deposited 2020-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
319–541（223 aa）
Chain F
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 LEU LEUCINE × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 6M1V Crystal structure of post fusion core of 2019-nCoV S2 subunit Deposited 2020-02-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
918–966（49 aa）
Chain A
1162–1203（42 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M bis-tris, pH 6.5, and 25% (wt/vol) polyethylene glycol 3350
|
Resolution 1.50 Å R-free 0.212 |
| 6VSB Prefusion 2019-nCoV spike glycoprotein with a single receptor-binding domain up Deposited 2020-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.46 Å |
| 6VW1 Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 Deposited 2020-02-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
455–518（64 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Tris, PEG 6000, and 100 mM NaCl.
|
Resolution 2.68 Å R-free 0.229 |
| 6VW1 Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 Deposited 2020-02-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
455–518（64 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Tris, PEG 6000, and 100 mM NaCl.
|
Resolution 2.68 Å R-free 0.229 |
| 6VXX Structure of the SARS-CoV-2 spike glycoprotein (closed state) Deposited 2020-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Fragment：ectodomain
Chain B
14–1211（1198 aa）
Fragment：ectodomain
Chain C
14–1211（1198 aa）
Fragment：ectodomain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 6VYB SARS-CoV-2 spike ectodomain structure (open state) Deposited 2020-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Fragment：ectodomain
Chain B
14–1211（1198 aa）
Fragment：ectodomain
Chain C
14–1211（1198 aa）
Fragment：ectodomain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6W41 Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody CR3022 Deposited 2020-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | GOL GLYCEROL × 1 SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；80 mM sodium acetate pH 4.6, 1.5 M ammonium sulfate, and 20% glycerol
|
Resolution 3.08 Å R-free 0.243 |
| 6WPS Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment Deposited 2020-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Fragment：;signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag,signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag
;
Chain B
14–1211（1198 aa）
Fragment：;signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag,signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag
;
Chain E
14–1211（1198 aa）
Fragment：;signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag,signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag
;
|
Mutation：R701S,R702G,R704G,K1005P,V1005P Mutation：R701S,R702G,R704G,K1005P,V1005P Mutation：R701S,R702G,R704G,K1005P,V1005P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6WPT Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state) Deposited 2020-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
14–1211（1198 aa）
Fragment：;signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag,signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag
;
Chain B
14–1211（1198 aa）
Fragment：;signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag,signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag
;
Chain C
14–1211（1198 aa）
Fragment：;signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag,signaling sequence + ectodomain (UNP residues 14-1211) + foldon trimerization domain + TEV cleavage site + His-tag
;
|
Mutation：R701S,R702G,R704G,K1005P,V1005P Mutation：R701S,R702G,R704G,K1005P,V1005P Mutation：R701S,R702G,R704G,K1005P,V1005P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6X29 SARS-CoV-2 rS2d Down State Spike Protein Trimer Deposited 2020-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain B
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain C
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
|
Mutation：D985C+S383C Mutation：D985C+S383C Mutation：D985C+S383C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 6X2A SARS-CoV-2 u1S2q 1-RBD Up Spike Protein Trimer Deposited 2020-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain B
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain C
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
|
Mutation：F855Y+N856I+A570L+T572I Mutation：F855Y+N856I+A570L+T572I Mutation：F855Y+N856I+A570L+T572I | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6X2B SARS-CoV-2 u1S2q 2-RBD Up Spike Protein Trimer Deposited 2020-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain B
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain C
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
|
Mutation：F855Y+N856I+A570L+T572I Mutation：F855Y+N856I+A570L+T572I Mutation：F855Y+N856I+A570L+T572I | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 6X2C SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer Deposited 2020-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain B
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain C
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
|
Mutation：F855Y+N856I+A570L+T572I Mutation：F855Y+N856I+A570L+T572I Mutation：F855Y+N856I+A570L+T572I | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 6X45 SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE) Deposited 2020-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
912–966（55 aa）
Chain B
912–966（55 aa）
Chain C
912–966（55 aa）
Chain D
1168–1203（36 aa）
Chain E
1168–1203（36 aa）
Chain F
1168–1203（36 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G1171Q, Q1180E, K1181Y, D1184K, R1185K, N1187E, N1192K, N1194E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G1171Q, Q1180E, K1181Y, D1184K, R1185K, N1187E, N1192K, N1194E Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G1171Q, Q1180E, K1181Y, D1184K, R1185K, N1187E, N1192K, N1194E Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Peptide solution: Lyophilized TFA salt dissolved in 1% w/v beta-D-octylglucoside; HRN (4 mg/mL), HRC-QEYKKEKE (3 mg/mL)
Well solution: 0.1 M Tris pH 7.8, 26% w/v PEG3350, 0.3 M MgCl2
Drop: 1 uL peptide solution, 1 uL well solution
Reservoir: 150 uL in VDXm plate
|
Resolution 2.20 Å R-free 0.278 |
| 6X6P Characterization of the SARS-CoV-2 S Protein: Biophysical, Biochemical, Structural, and Antigenic Analysis Deposited 2020-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–1208（1194 aa）
Chain B
15–1208（1194 aa）
Chain C
15–1208（1194 aa）
|
Mutation：R682G R683S R685S K986P V987P Mutation：R682G R683S R685S K986P V987P Mutation：R682G R683S R685S K986P V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 6X79 Prefusion SARS-CoV-2 S ectodomain trimer covalently stabilized in the closed conformation Deposited 2020-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Fragment：ectodomain(UNP residues 14-1211)
Chain B
14–1211（1198 aa）
Fragment：ectodomain(UNP residues 14-1211)
Chain C
14–1211（1198 aa）
Fragment：ectodomain(UNP residues 14-1211)
|
Mutation：S383C,D985C Mutation：S383C,D985C Mutation：S383C,D985C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 6XC2 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.1 Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1M sodium citrate pH 5.5
15% polyethylene glycol 6000
|
Resolution 3.11 Å R-free 0.267 |
| 6XC2 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.1 Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Z
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1M sodium citrate pH 5.5
15% polyethylene glycol 6000
|
Resolution 3.11 Å R-free 0.267 |
| 6XC3 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.1 and CR3022 Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；20% PEG 3000, 0.2 M sodium chloride, 0.1 M HEPES pH 7.5
|
Resolution 2.70 Å R-free 0.225 |
| 6XC4 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.3 Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1 M sodium phosphate pH 6.5
12% polyethylene glycol 8000
|
Resolution 2.34 Å R-free 0.219 |
| 6XC4 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC12.3 Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Z
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1 M sodium phosphate pH 6.5
12% polyethylene glycol 8000
|
Resolution 2.34 Å R-free 0.219 |
| 6XC7 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CC12.3 and CR3022 Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1M Tris pH 8
15% ethylene glycol
1M lithium chloride
10% PEG 6000
|
Resolution 2.88 Å R-free 0.259 |
| 6XCM Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 1) Deposited 2020-06-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3 microliters added, blotted for 3 s with 0 blot force
|
Resolution 3.42 Å |
| 6XCN Structure of the SARS-CoV-2 spike glycoprotein in complex with the C105 neutralizing antibody Fab fragment (state 2) Deposited 2020-06-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
Chain E
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3 microliters added, blotted for 3 s with 0 blot force
|
Resolution 3.66 Å |
| 6XDG Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralizing antibodies Deposited 2020-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
319–541（223 aa）
Fragment：receptor binding domain (UNP residues 319-541)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 6XE1 Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a potent neutralizing antibody, CV30 Fab Deposited 2020-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–591（273 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M ammonium citrate, tribasic, 12% PEG 3350
|
Resolution 2.75 Å R-free 0.239 |
| 6XEY Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-4 Deposited 2020-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 6XF5 Cryo-EM structure of a biotinylated SARS-CoV-2 spike probe in the prefusion state (RBDs down) Deposited 2020-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 6XF6 Cryo-EM structure of a biotinylated SARS-CoV-2 spike probe in the prefusion state (1 RBD up) Deposited 2020-06-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 6XKL SARS-CoV-2 HexaPro S One RBD up Deposited 2020-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 6XKP Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270 Deposited 2020-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1 M sodium cacodylate pH 6.5
0.2 M sodium chloride
2 M ammonium sulfate
15% (v/v) ethylene glycol
|
Resolution 2.72 Å R-free 0.269 |
| 6XKP Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-270 Deposited 2020-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1 M sodium cacodylate pH 6.5
0.2 M sodium chloride
2 M ammonium sulfate
15% (v/v) ethylene glycol
|
Resolution 2.72 Å R-free 0.269 |
| 6XKQ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CV07-250 Deposited 2020-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.085 M HEPES pH 7.5
10% (v/v) ethylene glycol
15% (v/v) glycerol
8.5% (v/v) 2-propanol
17% (w/v) polyethylene glycol 4000
|
Resolution 2.55 Å R-free 0.255 |
| 6XLU Structure of SARS-CoV-2 spike at pH 4.0 Deposited 2020-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 6XM0 Consensus structure of SARS-CoV-2 spike at pH 5.5 Deposited 2020-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 6XM3 Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 1 Deposited 2020-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 6XM4 Structure of SARS-CoV-2 spike at pH 5.5, single RBD up, conformation 2 Deposited 2020-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 6XM5 Structure of SARS-CoV-2 spike at pH 5.5, all RBDs down Deposited 2020-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6XR8 Distinct conformational states of SARS-CoV-2 spike protein Deposited 2020-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 6XRA Distinct conformational states of SARS-CoV-2 spike protein Deposited 2020-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MAN alpha-D-mannopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 6XS6 SARS-CoV-2 Spike D614G variant, minus RBD Deposited 2020-07-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 6YLA Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab Deposited 2020-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–532（203 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 8 MLI MALONATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium malonate, 0.1 M Tris pH 8.0 and 30% w/v Polyethylene glycol 1,000
|
Resolution 2.42 Å R-free 0.237 |
| 6YLA Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab Deposited 2020-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
330–532（203 aa）
|
Not recorded | DMS DIMETHYL SULFOXIDE × 6 MLI MALONATE ION × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 1PE PENTAETHYLENE GLYCOL × 1 PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium malonate, 0.1 M Tris pH 8.0 and 30% w/v Polyethylene glycol 1,000
|
Resolution 2.42 Å R-free 0.237 |
| 6YM0 Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab (crystal form 1) Deposited 2020-04-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–532（203 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Sodium malonate, 0.1 M Tris pH 8.0 and 30% w/v Polyethylene glycol 1,000.
|
Resolution 4.36 Å R-free 0.319 |
| 6YOR Structure of the SARS-CoV-2 spike S1 protein in complex with CR3022 Fab Deposited 2020-04-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–532（203 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris pH 8.0, 200 mM NaCl, 0.02 % NaN3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 6YOR Structure of the SARS-CoV-2 spike S1 protein in complex with CR3022 Fab Deposited 2020-04-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
330–532（203 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris pH 8.0, 200 mM NaCl, 0.02 % NaN3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 6YZ5 H11-D4 complex with SARS-CoV-2 RBD Deposited 2020-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 12 ACT ACETATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol.
|
Resolution 1.80 Å R-free 0.193 |
| 6YZ7 H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex Deposited 2020-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain AAA
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；298 K；The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.
|
Resolution 3.30 Å R-free 0.269 |
| 6YZ7 H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex Deposited 2020-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain EEE
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；298 K；The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.
|
Resolution 3.30 Å R-free 0.269 |
| 6Z2M H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex Deposited 2020-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；Purified RBD, Fab CR3022 and nanobody H11-D4 were mixed together at a molar ratio of 1:1:1 to a final concentration of approximately 7 mg/ml and incubated at room temperature for one hour. Initial screening was performed in 96-well plates using the nanolitre sitting-drop vapour diffusion method. The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.
|
Resolution 2.71 Å R-free 0.241 |
| 6Z2M H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex Deposited 2020-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；Purified RBD, Fab CR3022 and nanobody H11-D4 were mixed together at a molar ratio of 1:1:1 to a final concentration of approximately 7 mg/ml and incubated at room temperature for one hour. Initial screening was performed in 96-well plates using the nanolitre sitting-drop vapour diffusion method. The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.
|
Resolution 2.71 Å R-free 0.241 |
| 6Z43 Cryo-EM Structure of SARS-CoV-2 Spike : H11-D4 Nanobody Complex Deposited 2020-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 6 seconds with a blotting force of -1
|
Resolution 3.30 Å |
| 6Z97 Structure of the prefusion SARS-CoV-2 spike glycoprotein Deposited 2020-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.40 Å |
| 6ZB4 SARS CoV-2 Spike protein, Closed conformation, C1 symmetry Deposited 2020-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.03 Å |
| 6ZB5 SARS CoV-2 Spike protein, Closed conformation, C3 symmetry Deposited 2020-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.85 Å |
| 6ZBP H11-H4 complex with SARS-CoV-2 Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain EEE
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Crystals were grown at using the sitting drop vapor diffusion method by mixing 0.2 uL of the 18 mg/mL H11-H4 RBD complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000. The crystals grew overnight and were flash cooled in a solution containing the mother liquor with 30 % (v/v) ethylene glycol.
|
Resolution 1.85 Å R-free 0.217 |
| 6ZCZ Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in ternary complex with EY6A Fab and a nanobody. Deposited 2020-06-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 5 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25 % (w/v) PEG 3350, 0.2 M NaCl, 0.1 M Tris pH 8.5
|
Resolution 2.65 Å R-free 0.260 |
| 6ZDG Association of three complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab Deposited 2020-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
333–526（194 aa）
Chain D
333–526（194 aa）
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.70 Å |
| 6ZDH SARS-CoV-2 Spike glycoprotein in complex with a neutralizing antibody EY6A Fab Deposited 2020-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.70 Å |
| 6ZER Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with EY6A Fab Deposited 2020-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.02 M NaH2PO4, 0.98 M K2HPO4
|
Resolution 3.80 Å R-free 0.251 |
| 6ZER Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with EY6A Fab Deposited 2020-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.02 M NaH2PO4, 0.98 M K2HPO4
|
Resolution 3.80 Å R-free 0.251 |
| 6ZER Crystal structure of receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with EY6A Fab Deposited 2020-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.02 M NaH2PO4, 0.98 M K2HPO4
|
Resolution 3.80 Å R-free 0.251 |
| 6ZFO Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab Deposited 2020-06-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.40 Å |
| 6ZFO Association of two complexes of largely structurally disordered Spike ectodomain with bound EY6A Fab Deposited 2020-06-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.40 Å |
| 6ZGE Uncleavable Spike Protein of SARS-CoV-2 in Closed Conformation Deposited 2020-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 6ZGG Furin Cleaved Spike Protein of SARS-CoV-2 with One RBD Erect Deposited 2020-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6ZGH Furin Cleaved Spike Protein of SARS-CoV-2 in Intermediate Conformation Deposited 2020-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.80 Å |
| 6ZGI Furin Cleaved Spike Protein of SARS-CoV-2 in Closed Conformation Deposited 2020-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 6ZH9 Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2) Deposited 2020-06-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain EEE
332–528（197 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；mixing 0.2 uL of the 18 mg/mL complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000.
|
Resolution 3.31 Å R-free 0.305 |
| 6ZHD H11-H4 bound to Spike Deposited 2020-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；50 mM Tris, pH 7, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 90 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 81 % relative humidity and ambient temperature.
|
Resolution 3.70 Å |
| 6ZLR Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex. Deposited 2020-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain EEE
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.7；293 K；0.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000
|
Resolution 3.10 Å R-free 0.247 |
| 6ZLR Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex. Deposited 2020-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain AAA
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.7；293 K；0.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000
|
Resolution 3.10 Å R-free 0.247 |
| 6ZLR Soaking competent crystal form of the SARS-CoV-2 Receptor Binding Domain (RBD):CR3022 complex. Deposited 2020-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain DDD
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.7；293 K；0.1 M SODIUM MALONATE, 0.1 M TRIS PH 7.7, 22% W/V POLYETHYLENE GLYCOL 1,000
|
Resolution 3.10 Å R-free 0.247 |
| 6ZOW SARS-CoV-2 spike in prefusion state Deposited 2020-07-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain a
1–1208（1208 aa）
|
Mutation：K986P, E987P Mutation：K986P, E987P Mutation：K986P, E987P Mutation：K986P, E987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 MAN alpha-D-mannopyranose × 2 DMS DIMETHYL SULFOXIDE × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 6ZOX Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x2 disulphide-bond mutant, G413C, V987C, single Arg S1/S2 cleavage site) Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：G413C, V987C, Single Arg S1/S2 cleavage site Mutation：G413C, V987C, Single Arg S1/S2 cleavage site Mutation：G413C, V987C, Single Arg S1/S2 cleavage site | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 6ZOY Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Closed State Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：S383C, D985C, K986P, V987P, Single Arg S1/S2 cleavage site Mutation：S383C, D985C, K986P, V987P, Single Arg S1/S2 cleavage site Mutation：S383C, D985C, K986P, V987P, Single Arg S1/S2 cleavage site | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6ZOZ Structure of Disulphide-stabilized SARS-CoV-2 Spike Protein Trimer (x1 disulphide-bond mutant, S383C, D985C, K986P, V987P, single Arg S1/S2 cleavage site) in Locked State Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：S383C, D985C, K986P, V987P, Single Arg S1/S2 cleavage site Mutation：S383C, D985C, K986P, V987P, Single Arg S1/S2 cleavage site Mutation：S383C, D985C, K986P, V987P, Single Arg S1/S2 cleavage site | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 BLA BILIVERDINE IX ALPHA × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6ZP0 Structure of SARS-CoV-2 Spike Protein Trimer (single Arg S1/S2 cleavage site) in Closed State Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：Single Arg S1/S2 Cleavage site Mutation：Single Arg S1/S2 Cleavage site Mutation：Single Arg S1/S2 Cleavage site | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 6ZP1 Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Closed State Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：K986P, V987P, Single Arg S1/S2 cleavage site Mutation：K986P, V987P, Single Arg S1/S2 cleavage site Mutation：K986P, V987P, Single Arg S1/S2 cleavage site | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6ZP2 Structure of SARS-CoV-2 Spike Protein Trimer (K986P, V987P, single Arg S1/S2 cleavage site) in Locked State Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1141（1128 aa）
Chain B
14–1141（1128 aa）
Chain C
14–1141（1128 aa）
|
Mutation：K986P, V987P, Single Arg S1/S2 cleavage site Mutation：K986P, V987P, Single Arg S1/S2 cleavage site Mutation：K986P, V987P, Single Arg S1/S2 cleavage site | BLA BILIVERDINE IX ALPHA × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6ZP5 SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation) Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 MAN alpha-D-mannopyranose × 2 DMS DIMETHYL SULFOXIDE × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 6ZP7 SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up open conformation) Deposited 2020-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 MAN alpha-D-mannopyranose × 2 DMS DIMETHYL SULFOXIDE × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 6ZWV Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: 3 Closed RBDs Deposited 2020-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 6ZXN Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1) Deposited 2020-07-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 7A25 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) Deposited 2020-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1146（1146 aa）
Chain B
1–1146（1146 aa）
Chain C
1–1146（1146 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 7A29 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation Deposited 2020-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 7A4N Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(S-closed trimer) Deposited 2020-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614N,R682S,R685G,A892P,A942P,V987P Mutation：D614N,R682S,R685G,A892P,A942P,V987P Mutation：D614N,R682S,R685G,A892P,A942P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 7A5R Complex of SARS-CoV-2 spike and CR3022 Fab (Non-Uniform Refinement) Deposited 2020-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7A5S Complex of SARS-CoV-2 spike and CR3022 Fab (Homogeneous Refinement) Deposited 2020-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7A91 Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement) Deposited 2020-09-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–685（685 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7A92 Dissociated S1 domain of SARS-CoV-2 Spike bound to ACE2 (Unmasked Refinement) Deposited 2020-09-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–676（676 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7A93 SARS-CoV-2 Spike Glycoprotein with 2 RBDs Erect Deposited 2020-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.90 Å |
| 7A94 SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound Deposited 2020-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7A95 SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound and 1 RBD Erect in Clockwise Direction Deposited 2020-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7A96 SARS-CoV-2 Spike Glycoprotein with 1 ACE2 Bound and 1 RBD Erect in Anticlockwise Direction Deposited 2020-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 7A97 SARS-CoV-2 Spike Glycoprotein with 2 ACE2 Bound Deposited 2020-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7A98 SARS-CoV-2 Spike Glycoprotein with 3 ACE2 Bound Deposited 2020-09-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.40 Å |
| 7AD1 Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G, A892P, A942P and V987P)(One up trimer) Deposited 2020-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.92 Å |
| 7AKD Structure of the SARS-CoV-2 spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment Deposited 2020-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 FUC alpha-L-fucopyranose × 3 MAN alpha-D-mannopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7B14 Nanobody E bound to Spike-RBD in a localized reconstruction Deposited 2020-11-23 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–528（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.79 Å |
| 7B17 SARS-CoV-spike RBD bound to two neutralising nanobodies. Deposited 2020-11-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–528（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.01 Å |
| 7B18 SARS-CoV-spike bound to two neutralising nanobodies Deposited 2020-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.62 Å |
| 7B3O Crystal structure of the SARS-CoV-2 RBD in complex with STE90-C11 Fab Deposited 2020-12-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
331–524（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；298 K；13.3% (w/v) polyethylene glycol 6,000,
0.1M MES pH 5.6
0.24M tri sodium citrate
|
Resolution 2.00 Å R-free 0.225 |
| 7B62 Crystal structure of SARS-CoV-2 spike protein N-terminal domain in complex with biliverdin Deposited 2020-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–311（311 aa）
|
Not recorded | BLA BILIVERDINE IX ALPHA × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 3 PGE TRIETHYLENE GLYCOL × 3 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；24% PEG 3350 (w/v) and 0.25 M NaSCN
|
Resolution 1.82 Å R-free 0.200 |
| 7BEH Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab Deposited 2020-12-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M MgCl2, 0.1 M bis-Tris pH 5.5 and 25 % (w/v) PEG 3350
|
Resolution 2.30 Å R-free 0.230 |
| 7BEI Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab Deposited 2020-12-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–528（196 aa）
|
Not recorded | NO3 NITRATE ION × 3 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.09 M of NPS (nitrate, phosphate and sulphate), 0.1 M MES/imidazole pH 6.5, 10% (w/v) PEG 8000 and 20% (v/v) ethylene glycol
|
Resolution 2.30 Å R-free 0.232 |
| 7BEJ Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 1) Deposited 2020-12-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 2 FMT FORMIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；containing 3.5 M NaCOOH pH 7.0
|
Resolution 2.42 Å R-free 0.231 |
| 7BEK Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-158 Fab (crystal form 2) Deposited 2020-12-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–528（196 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 3 GOL GLYCEROL × 3 SO4 SULFATE ION × 2 CL CHLORIDE ION × 6 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；294 K；0.15 M (NH4)2SO4, 0.1 M Tris pH 7.6 and 14.6% (w/v) PEG 4000
|
Resolution 2.04 Å R-free 0.220 |
| 7BEL Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs Deposited 2020-12-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
333–528（196 aa）
|
Not recorded | ACT ACETATE ION × 1 GOL GLYCEROL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.15 M (NH4)2SO4, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 4000
|
Resolution 2.53 Å R-free 0.286 |
| 7BEL Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-88 and COVOX-45 Fabs Deposited 2020-12-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain X
333–528（196 aa）
|
Not recorded | ACT ACETATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；0.15 M (NH4)2SO4, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 4000
|
Resolution 2.53 Å R-free 0.286 |
| 7BEM Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 scFv Deposited 2020-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 2 CL CHLORIDE ION × 2 PO4 PHOSPHATE ION × 2 PRO PROLINE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.2 M Proline, 0.1 M HEPES pH 7.5 and 10% (w/v) PEG 3350
|
Resolution 2.52 Å R-free 0.247 |
| 7BEN Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs Deposited 2020-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | IMD IMIDAZOLE × 2 GOL GLYCEROL × 4 BR BROMIDE ION × 6 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.1 M BIS-TRIS pH 6.5, 16% (w/v) PEG 10000
|
Resolution 2.50 Å R-free 0.282 |
| 7BEN Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253 and COVOX-75 Fabs Deposited 2020-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
333–528（196 aa）
|
Not recorded | IMD IMIDAZOLE × 2 GOL GLYCEROL × 1 BR BROMIDE ION × 8 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 IOD IODIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.1 M BIS-TRIS pH 6.5, 16% (w/v) PEG 10000
|
Resolution 2.50 Å R-free 0.282 |
| 7BEO Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs Deposited 2020-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
333–528（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 ACT ACETATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；0.1 M ammonium acetate, 0.1 M bis-Tris pH 5.5 and 17% (w/v) PEG 10000
|
Resolution 3.19 Å R-free 0.274 |
| 7BEO Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-253H55L and COVOX-75 Fabs Deposited 2020-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain X
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 1 ACT ACETATE ION × 5 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；0.1 M ammonium acetate, 0.1 M bis-Tris pH 5.5 and 17% (w/v) PEG 10000
|
Resolution 3.19 Å R-free 0.274 |
| 7BEP Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs Deposited 2020-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | IMD IMIDAZOLE × 3 CL CHLORIDE ION × 5 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 3 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；containing 0.1 M amino acids (Glu, Ala, Gly, Lys, Ser), 0.1 M MES/imidazole/ pH 6.5, 10% (w/v) PEG 20000 and 20% (w/v) PEG MME 550.
|
Resolution 2.61 Å R-free 0.241 |
| 7BEP Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in a ternary complex with COVOX-384 and S309 Fabs Deposited 2020-12-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
333–528（196 aa）
|
Not recorded | IMD IMIDAZOLE × 2 CL CHLORIDE ION × 5 GLU GLUTAMIC ACID × 1 GLY GLYCINE × 3 GOL GLYCEROL × 3 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；containing 0.1 M amino acids (Glu, Ala, Gly, Lys, Ser), 0.1 M MES/imidazole/ pH 6.5, 10% (w/v) PEG 20000 and 20% (w/v) PEG MME 550.
|
Resolution 2.61 Å R-free 0.241 |
| 7BH9 SARS-CoV-2 RBD-62 in complex with ACE2 peptidase domain Deposited 2021-01-11 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–528（196 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7BNM Closed conformation of D614G SARS-CoV-2 spike protein Deposited 2021-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1146（1146 aa）
Chain B
1–1146（1146 aa）
Chain C
1–1146（1146 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7BNN Open conformation of D614G SARS-CoV-2 spike with 1 Erect RBD Deposited 2021-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7BNO Open conformation of D614G SARS-CoV-2 spike with 2 Erect RBDs Deposited 2021-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1146（1146 aa）
Chain B
1–1146（1146 aa）
Chain C
1–1146（1146 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7BWJ crystal structure of SARS-CoV-2 antibody with RBD Deposited 2020-04-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–529（211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M magnesium formate dihydrate, 0.1M sodium acetate trihydrate, pH 4.0, 18% PEG 5000 mme
|
Resolution 2.85 Å R-free 0.264 |
| 7BYR BD23-Fab in complex with the S ectodomain trimer Deposited 2020-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683G, R685S, K986P, V987P Mutation：R682G, R683G, R685S, K986P, V987P Mutation：R682G, R683G, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
| 7BZ5 Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody Deposited 2020-04-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.15 M ammonium sulfate, 0.1 M MES pH 6, 15% w/v PEG 400
|
Resolution 1.84 Å R-free 0.191 |
| 7C01 Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD Deposited 2020-04-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；24 % w/v PEG 1500, 20 % v/v Glycerol
|
Resolution 2.88 Å R-free 0.265 |
| 7C01 Molecular basis for a potent human neutralizing antibody targeting SARS-CoV-2 RBD Deposited 2020-04-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；24 % w/v PEG 1500, 20 % v/v Glycerol
|
Resolution 2.88 Å R-free 0.265 |
| 7C2L S protein of SARS-CoV-2 in complex bound with 4A8 Deposited 2020-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7C53 Crystal Structure of SARS-CoV-2 HR1 motif in complex with pan-CoVs inhibitor EK1 Deposited 2020-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
910–975（66 aa）
Fragment：HR1 motif
Chain B
910–975（66 aa）
Fragment：HR1 motif
Chain C
910–975（66 aa）
Fragment：HR1 motif
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；30% MPD, 0.1 M Na Acetate pH 5.0, 0.02 M Calcium Chloride
|
Resolution 2.28 Å R-free 0.242 |
| 7C53 Crystal Structure of SARS-CoV-2 HR1 motif in complex with pan-CoVs inhibitor EK1 Deposited 2020-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain D
910–975（66 aa）
Fragment：HR1 motif
Chain E
910–975（66 aa）
Fragment：HR1 motif
Chain F
910–975（66 aa）
Fragment：HR1 motif
|
Not recorded | CA CALCIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；30% MPD, 0.1 M Na Acetate pH 5.0, 0.02 M Calcium Chloride
|
Resolution 2.28 Å R-free 0.242 |
| 7C8D Cryo-EM structure of cat ACE2 and SARS-CoV-2 RBD Deposited 2020-05-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
|
Resolution 3.00 Å |
| 7C8J Structural basis for cross-species recognition of COVID-19 virus spike receptor binding domain to bat ACE2 Deposited 2020-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：UNP residues 333-527
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Succinic acid pH 7.0, 0.1 M BICINE pH 8.5, 30% v/v Polyethylene glycol monomethyl ether 550
|
Resolution 3.18 Å R-free 0.271 |
| 7C8V Structure of sybody SR4 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD) Deposited 2020-06-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–531（202 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3000, 100mM HEPES pH 7.5, 200mM sodium chloride
|
Resolution 2.15 Å R-free 0.224 |
| 7C8W Structure of sybody MR17 in complex with the SARS-CoV-2 S receptor-binding domain (RBD) Deposited 2020-06-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–531（202 aa）
Fragment：Receptor binding domain
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M magnesium formate dihydrate, 20% w/v polyethylene glycol 3350
|
Resolution 2.77 Å R-free 0.267 |
| 7CAB Structural basis for neutralization of SARS-CoV-2 and SARS-CoV by a potent therapeutic antibody Deposited 2020-06-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain B
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain C
1–1208（1208 aa）
Fragment：UNP residues 1-1208
|
Mutation：R682G, R683S, R685S, K835M, T844M, A846Y, D848A, L849M, I850Q, C851M, Q853Y, K854R K986P, V987P Mutation：R682G, R683S, R685S, K835M, T844M, A846Y, D848A, L849M, I850Q, C851M, Q853Y, K854R K986P, V987P Mutation：R682G, R683S, R685S, K835M, T844M, A846Y, D848A, L849M, I850Q, C851M, Q853Y, K854R K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7CAC SARS-CoV-2 S trimer with one RBD in the open state and complexed with one H014 Fab. Deposited 2020-06-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K835M, T844M, A846Y, C851M, Q853Y, K854R K986P, V987P Mutation：R682G, R683S, R685S, K835M, T844M, A846Y, C851M, Q853Y, K854R K986P, V987P Mutation：R682G, R683S, R685S, K835M, T844M, A846Y, C851M, Q853Y, K854R K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 7CAH The interface of H014 Fab binds to SARS-CoV-2 S Deposited 2020-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7CAI SARS-CoV-2 S trimer with two RBDs in the open state and complexed with two H014 Fab Deposited 2020-06-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain B
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain C
1–1208（1208 aa）
Fragment：UNP residues 1-1208
|
Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 7CAK SARS-CoV-2 S trimer with three RBD in the open state and complexed with three H014 Fab Deposited 2020-06-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain B
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain C
1–1208（1208 aa）
Fragment：UNP residues 1-1208
|
Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 7CAN Structure of sybody MR17-K99Y in complex with the SARS-CoV-2 S Receptor-binding domain (RBD) Deposited 2020-06-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–531（202 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M MgCl2, 20% PEG 3350
|
Resolution 2.94 Å R-free 0.267 |
| 7CDI Crystal structure of SARS-CoV-2 antibody P2C-1F11 with RBD Deposited 2020-06-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1M sodium citrate tribasic dihydrate, pH 5.8, 20% PEG 6000
|
Resolution 2.96 Å R-free 0.254 |
| 7CDJ Crystal structure of SARS-CoV-2 antibody P2C-1A3 with RBD Deposited 2020-06-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1M lithium sulfate monohydrate, 0.1M citric acid, pH 3.5, 18% PEG 6000
|
Resolution 3.40 Å R-free 0.271 |
| 7CH4 Crystal structure of the SARS-CoV-2 S RBD in complex with BD-604 Fab Deposited 2020-07-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Potassium phosphate dibasic(pH 9.2),20% w/v Polyethylene glycol 3350
|
Resolution 3.15 Å R-free 0.273 |
| 7CH5 Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab Deposited 2020-07-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0 and 18% w/v Polyethylene glycol 20000
|
Resolution 2.70 Å R-free 0.260 |
| 7CHB Crystal structure of the SARS-CoV-2 RBD in complex with BD-236 Fab Deposited 2020-07-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium Citrate, pH 5.0, 8% (w/v) PEG 8000
|
Resolution 2.40 Å R-free 0.226 |
| 7CHC Crystal structure of the SARS-CoV-2 S RBD in complex with BD-629 Fab and BD-368-2 Fab Deposited 2020-07-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Imidazole pH 7.0 and 20% w/v Polyethylene glycol 6000
|
Resolution 2.71 Å R-free 0.286 |
| 7CHE Crystal structure of the SARS-CoV-2 RBD in complex with BD-236 Fab and BD-368-2 Fab Deposited 2020-07-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M sodium acetate pH 4.0 and 10% (w/v) Polyethylene glycol monomethyl ether 2,000
|
Resolution 3.42 Å R-free 0.239 |
| 7CHF Crystal structure of the SARS-CoV-2 RBD in complex with BD-604 Fab and BD-368-2 Fab Deposited 2020-07-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium sulfate and 12% (w/v) polyethylene glycol 8000
|
Resolution 2.67 Å R-free 0.270 |
| 7CHH Cryo-EM structure of the SARS-CoV-2 S-6P in complex with BD-368-2 Fabs Deposited 2020-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 7CHO Crystal structure of SARS-CoV-2 antibody P5A-1D2 with RBD Deposited 2020-07-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Magnesium chloride hexahydrate, 0.1M Tris, pH 8.5, 3.4M 1,6-Hexanediol
|
Resolution 2.56 Å R-free 0.247 |
| 7CHO Crystal structure of SARS-CoV-2 antibody P5A-1D2 with RBD Deposited 2020-07-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Magnesium chloride hexahydrate, 0.1M Tris, pH 8.5, 3.4M 1,6-Hexanediol
|
Resolution 2.56 Å R-free 0.247 |
| 7CHP Crystal structure of SARS-CoV-2 antibody P5A-3C8 with RBD Deposited 2020-07-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES, pH 7.5, 25% w/v PEG 3350
|
Resolution 2.36 Å R-free 0.220 |
| 7CHS Crystal structure of SARS-CoV-2 antibody P22A-1D1 with RBD Deposited 2020-07-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.1M potassium chloride, 0.1M NaHEPES, pH 7.0, 15% PEG 5000MME
|
Resolution 2.40 Å R-free 0.224 |
| 7CJF Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody Fab Deposited 2020-07-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
334–527（194 aa）
Fragment：receptor binding domain, RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293 K；20%(w/v)PEG 3350
0.2M potassium citrate tribasic
|
Resolution 2.11 Å R-free 0.229 |
| 7CM4 Crystal Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody CT-P59 Deposited 2020-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–536（218 aa）
|
Not recorded | NI NICKEL (II) ION × 2 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293.15 K；100 mM Tris-Cl pH 8.0
16% (w/v) Polyethylene glycol monomethyl ether 2,000
10 mM Nickel(II) Chloride hexahydrate
|
Resolution 2.71 Å R-free 0.242 |
| 7CN9 Cryo-EM structure of SARS-CoV-2 Spike ectodomain Deposited 2020-07-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1140（1127 aa）
Chain B
14–1140（1127 aa）
Chain C
14–1140（1127 aa）
|
Mutation：R682G, R683S, R685G, K986P, V986P Mutation：R682G, R683S, R685G, K986P, V986P Mutation：R682G, R683S, R685G, K986P, V986P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.70 Å |
| 7COT Structure of post fusion core of SARS-CoV-2 S2 subunit Deposited 2020-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
910–988（79 aa）
Chain A
1162–1206（45 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；25% PEG 3350, 0.07M Bis-Tris propane pH 8.5, 0.03M citric acid
|
Resolution 2.16 Å R-free 0.247 |
| 7COT Structure of post fusion core of SARS-CoV-2 S2 subunit Deposited 2020-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain B
910–988（79 aa）
Chain B
1162–1206（45 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；25% PEG 3350, 0.07M Bis-Tris propane pH 8.5, 0.03M citric acid
|
Resolution 2.16 Å R-free 0.247 |
| 7COT Structure of post fusion core of SARS-CoV-2 S2 subunit Deposited 2020-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain C
910–988（79 aa）
Chain C
1162–1206（45 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；283 K；25% PEG 3350, 0.07M Bis-Tris propane pH 8.5, 0.03M citric acid
|
Resolution 2.16 Å R-free 0.247 |
| 7CT5 S protein of SARS-CoV-2 in complex bound with T-ACE2 Deposited 2020-08-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：P986K, P987V Mutation：P986K, P987V Mutation：P986K, P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7CWL SARS-CoV-2 spike protein and P17 fab complex with one RBD in close state Deposited 2020-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7CWM Complex of SARS-CoV-2 spike protein and Fab P17 with one RBD in open state and two RBD in closed state Deposited 2020-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7CWN P17-H014 Fab cocktail in complex with SARS-CoV-2 spike protein Deposited 2020-08-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7CWO SARS-CoV-2 spike protein RBD and P17 fab complex Deposited 2020-08-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7CWS SARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fabs Cocktail Deposited 2020-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain O
14–1147（1134 aa）
Chain Q
14–1147（1134 aa）
Chain R
14–1147（1134 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7CWT SARS-CoV-2 Spike protein in complex with hb27 and fc05 Fab cocktail Deposited 2020-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7CWU SARS-CoV-2 spike proteins trimer in complex with P17 and FC05 Fabs cocktail Deposited 2020-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 30-meric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7CYH Binding interface of SARS-CoV-2 RBD and its neutralizing antibody HB27 Deposited 2020-09-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7CYP Complex of SARS-CoV-2 spike trimer with its neutralizing antibody HB27 Deposited 2020-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: 24-meric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P Mutation：R682G, R683S, R685S, K835M, I844M, A846Y, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7CYV Crystal structure of FD20, a neutralizing single-chain variable fragment (scFv) in complex with SARS-CoV-2 Spike receptor-binding domain (RBD) Deposited 2020-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–531（202 aa）
Fragment：receptor-binding domain (RBD)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.2 M lithium sulfate monohydrate, 0.1 M Bis-Tris pH 5.5, 25% w/v polyethylene glycol 3350
|
Resolution 3.13 Å R-free 0.276 |
| 7CZP S protein of SARS-CoV-2 in complex bound with P2B-1A1 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7CZQ S protein of SARS-CoV-2 in complex bound with P2B-1A10 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7CZR S protein of SARS-CoV-2 in complex bound with P5A-1B8_2B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7CZS S protein of SARS-CoV-2 in complex bound with P5A-1B8_3B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7CZT S protein of SARS-CoV-2 in complex bound with P5A-2G9 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7CZU S protein of SARS-CoV-2 in complex bound with P5A-1B6_2B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7CZV S protein of SARS-CoV-2 in complex bound with P5A-1B6_3B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7CZW S protein of SARS-CoV-2 in complex bound with P5A-2G7 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7CZX S protein of SARS-CoV-2 in complex bound with P5A-1B9 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7CZY S protein of SARS-CoV-2 in complex bound with P5A-2F11_2B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7CZZ S protein of SARS-CoV-2 in complex bound with P5A-2F11_3B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7D00 S protein of SARS-CoV-2 in complex bound with FabP5A-1B8 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7D03 S protein of SARS-CoV-2 in complex bound with FabP5A-2G7 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7D0B S protein of SARS-CoV-2 in complex bound with P5A-3C12_1B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7D0C S protein of SARS-CoV-2 in complex bound with P5A-3A1 Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7D0D S protein of SARS-CoV-2 in complex bound with P5A-3C12_2B Deposited 2020-09-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7D2Z Structure of sybody SR31 in complex with the SARS-CoV-2 S Receptor Binding domain (RBD) Deposited 2020-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–531（202 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | FMT FORMIC ACID × 13 GOL GLYCEROL × 5 ACT ACETATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.0M sodium formate, 0.1M sodium acetate trihydrate pH 4.6
|
Resolution 1.97 Å R-free 0.207 |
| 7D30 Structure of sybody MR17-SR31 fusion in complex with the SARS-CoV-2 S Receptor Binding domain (RBD) Deposited 2020-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–531（202 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 5 ACT ACETATE ION × 14 1PE PENTAETHYLENE GLYCOL × 2 BU2 1,3-BUTANEDIOL × 5 CD CADMIUM ION × 17 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.1M cadmium chloride, 30% (v/v) PEG 400, 4%(v/v) 1,3-butanediol, 0.1M sodium acetate pH 4.5
|
Resolution 2.10 Å R-free 0.236 |
| 7D4G A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2 Deposited 2020-09-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
13–290（278 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7D6I A neutralizing MAb targeting receptor-binding-domain of SARS-CoV-2 Deposited 2020-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–532（214 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；50 mM Calcium chloride dihydrate, 100 mM BIS-TRIS pH 6.5, 30% v/v Polyethylene glycol and monomethyl ether 550
|
Resolution 3.41 Å R-free 0.255 |
| 7DCC S-3C1-F3b structure, all the three RBDs are in the up conformation and each of them associates with a 3C1 Fab Deposited 2020-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain E
1–1208（1208 aa）
Chain I
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7DCX S-3C1-F3a structure, two RBDs are up and one RBD is down, each RBD binds with a 3C1 fab. Deposited 2020-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.90 Å |
| 7DD2 S-3C1-F2 structure, two RBDs are up and one RBD is down, the two up RBD bind with a 3C1 fab. Deposited 2020-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.60 Å |
| 7DD8 S-3C1-F1 structure, one RBD is up and two RBDs are down, the up RBD binds with a 3C1 fab Deposited 2020-10-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.50 Å |
| 7DDD SARS-Cov2 S protein at close state Deposited 2020-10-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain B
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain C
1–1208（1208 aa）
Fragment：UNP residues 1-1208
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7DDN SARS-Cov2 S protein at open state Deposited 2020-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.30 Å |
| 7DEO Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–530（197 aa）
Fragment：RBD
|
Not recorded | CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；1% w/v Tryptone, 0.001M Sodium azide, 0.05M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.50 Å R-free 0.232 |
| 7DEO Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–530（197 aa）
Fragment：RBD
|
Not recorded | CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；1% w/v Tryptone, 0.001M Sodium azide, 0.05M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.50 Å R-free 0.232 |
| 7DET Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv Deposited 2020-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–530（197 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2M sodium chloride, 0.1M Tris pH 8.5, 29% w/v Polyethylene glycol 3350
|
Resolution 2.20 Å R-free 0.260 |
| 7DET Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv Deposited 2020-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
334–530（197 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2M sodium chloride, 0.1M Tris pH 8.5, 29% w/v Polyethylene glycol 3350
|
Resolution 2.20 Å R-free 0.260 |
| 7DEU Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv Deposited 2020-11-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–530（197 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.8M Potassium sodium tartrate tetrahydrate, 0.1M Tris pH 8.5, 0.5% w/v Polyethylene glycol monomethyl ether 5000
|
Resolution 2.10 Å R-free 0.229 |
| 7DF3 SARS-CoV-2 S trimer, S-closed Deposited 2020-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7DF4 SARS-CoV-2 S-ACE2 complex Deposited 2020-11-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7DHX Crystal structure of SARS-CoV-2 RBD binding to pangolin ACE2 Deposited 2020-11-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–527（209 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.05M potassium phosphate, 20% w/v Polyethylene glycol 8000
|
Resolution 2.30 Å R-free 0.235 |
| 7DJZ Crystal structure of SARS-CoV-2 Spike RBD in complex with MW01 Fab Deposited 2020-11-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
Fragment：Receptor Binding Domain
|
Not recorded | CIT CITRIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；0.1 M sodium citrate, pH 5.6, 18% (w/v) polyethylene glycol (PEG) 4000, 14% (v/v) 2-propanol, and 0.01 M barium chloride.
|
Resolution 2.40 Å R-free 0.230 |
| 7DK0 Crystal structure of SARS-CoV-2 Spike RBD in complex with MW05 Fab Deposited 2020-11-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M sodium citrate tribasic, 21% (w/v) PEG 3350, 0.02 M urea
|
Resolution 3.20 Å R-free 0.265 |
| 7DK2 Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab Deposited 2020-11-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；12% (w/v) polyethylene glycol 20000, 100 mM MES, pH 6.5, and 0.01 M TCEP
|
Resolution 3.00 Å R-free 0.304 |
| 7DK2 Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab Deposited 2020-11-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
319–541（223 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；12% (w/v) polyethylene glycol 20000, 100 mM MES, pH 6.5, and 0.01 M TCEP
|
Resolution 3.00 Å R-free 0.304 |
| 7DK2 Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab Deposited 2020-11-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
319–541（223 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；12% (w/v) polyethylene glycol 20000, 100 mM MES, pH 6.5, and 0.01 M TCEP
|
Resolution 3.00 Å R-free 0.304 |
| 7DK2 Crystal structure of SARS-CoV-2 Spike RBD in complex with MW07 Fab Deposited 2020-11-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
319–541（223 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；12% (w/v) polyethylene glycol 20000, 100 mM MES, pH 6.5, and 0.01 M TCEP
|
Resolution 3.00 Å R-free 0.304 |
| 7DK3 SARS-CoV-2 S trimer, S-open Deposited 2020-11-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.00 Å |
| 7DK4 S-2H2-F3a structure, two RBDs are up and one RBD is down, each RBD binds with a 2H2 Fab. Deposited 2020-11-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7DK5 S-2H2-F1 structure, one RBD is up and two RBDs are down, only up RBD binds with a 2H2 Fab Deposited 2020-11-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 13.50 Å |
| 7DK6 S-2H2-F2 structure, two RBDs are up and one RBD is down, each up RBD binds with a 2H2 Fab. Deposited 2020-11-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7DK7 S-2H2-F3b structure, three RBDs are up and each RBD binds with a 2H2 Fab. Deposited 2020-11-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.70 Å |
| 7DMU Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39 Deposited 2020-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–531（213 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.6 M ammonium sulfate, 0.25 M lithium sulfate, and 0.05 M CAPS pH 10.5
|
Resolution 3.20 Å R-free 0.198 |
| 7DMU Structure of SARS-CoV-2 spike receptor-binding domain complexed with high affinity ACE2 mutant 3N39 Deposited 2020-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
319–531（213 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.6 M ammonium sulfate, 0.25 M lithium sulfate, and 0.05 M CAPS pH 10.5
|
Resolution 3.20 Å R-free 0.198 |
| 7DPM Crystal structure of SARS-CoV-2 Spike RBD in complex with MW06 Fab Deposited 2020-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
Fragment：RBD domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3.5；289 K；12% EG, 0.1 M Citrate-Na, pH 3.5, 14% PEG 6000
|
Resolution 3.30 Å R-free 0.263 |
| 7DPM Crystal structure of SARS-CoV-2 Spike RBD in complex with MW06 Fab Deposited 2020-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
319–541（223 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3.5；289 K；12% EG, 0.1 M Citrate-Na, pH 3.5, 14% PEG 6000
|
Resolution 3.30 Å R-free 0.263 |
| 7DPM Crystal structure of SARS-CoV-2 Spike RBD in complex with MW06 Fab Deposited 2020-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
319–541（223 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3.5；289 K；12% EG, 0.1 M Citrate-Na, pH 3.5, 14% PEG 6000
|
Resolution 3.30 Å R-free 0.263 |
| 7DPM Crystal structure of SARS-CoV-2 Spike RBD in complex with MW06 Fab Deposited 2020-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
319–541（223 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3.5；289 K；12% EG, 0.1 M Citrate-Na, pH 3.5, 14% PEG 6000
|
Resolution 3.30 Å R-free 0.263 |
| 7DQA Cryo-EM structure of SARS-CoV2 RBD-ACE2 complex Deposited 2020-12-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–526（194 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7DWX Conformation 1 of S-ACE2-B0AT1 ternary complex Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 10 PDB declaration: decameric |
Chain E
1–1273（1273 aa）
Chain F
1–1273（1273 aa）
Chain G
1–1273（1273 aa）
Chain H
1–1273（1273 aa）
Chain I
1–1273（1273 aa）
Chain J
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 64 LEU LEUCINE × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.30 Å |
| 7DWY S protein of SARS-CoV-2 in the locked conformation Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 59 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7DWZ S protein of SARS-CoV-2 in the active conformation Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7DX0 Trypsin-digested S protein of SARS-CoV-2 Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7DX1 S protein of SARS-CoV-2 D614G mutant Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G, K986P, V987P Mutation：D614G, K986P, V987P Mutation：D614G, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7DX2 Trypsin-digested S protein of SARS-CoV-2 D614G mutant Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G, K986P, V987P Mutation：D614G, K986P, V987P Mutation：D614G, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7DX3 S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 1 (1 up RBD and no PD bound) Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7DX4 The structure of FC08 Fab-hA.CE2-RBD complex Deposited 2021-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7DX5 S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 2 (1 up RBD and 1 PD bound) Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7DX6 S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 3 (2 up RBD and 1 PD bound) Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7DX7 Trypsin-digested S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 1 (1 up RBD and 1 PD bound) Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7DX8 Trypsin-digested S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 2 (2 up RBD and 2 PD bound) Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7DX9 Trypsin-digested S protein of SARS-CoV-2 bound with PD of ACE2 in the conformation 3 (3 up RBD and 2 PD bound) Deposited 2021-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7DZW Apo spike protein from SARS-CoV2 Deposited 2021-01-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1254（1241 aa）
Chain B
14–1254（1241 aa）
Chain C
14–1254（1241 aa）
|
Mutation：D614G, R682G, R683S, R685G, K986P, V987P Mutation：D614G, R682G, R683S, R685G, K986P, V987P Mutation：D614G, R682G, R683S, R685G, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 7DZX Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 8D2 Deposited 2021-01-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Mutation：D614G, R682G, R683S, R685G, K986P, V987P Mutation：D614G, R682G, R683S, R685G, K986P, V987P Mutation：D614G, R682G, R683S, R685G, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 7DZY Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 2490 Deposited 2021-01-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1211（1185 aa）
Chain B
27–1211（1185 aa）
Chain C
27–1211（1185 aa）
|
Mutation：D614G, R682G, R683S, R685G, K986P, V987P Mutation：D614G, R682G, R683S, R685G, K986P, V987P Mutation：D614G, R682G, R683S, R685G, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7E23 SARS-CoV-2 spike in complex with the CA521 neutralizing antibody Fab (focused refinement on Fab-RBD) Deposited 2021-02-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7E39 SARS-CoV-2 spike in complex with the Ab4 neutralizing antibody (State 3) Deposited 2021-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7E3B SARS-Cov-2 spike in complex with the Ab5 neutralizing antibody (focused refinement on Fab-RBD) Deposited 2021-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7E3C SARS-CoV-2 spike in complex with the Ab1 neutralizing antibody (focused refinement on Fab-RBD) Deposited 2021-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7E3J Crystal structure of SARS-CoV-2 RBD binding to dog ACE2 Deposited 2021-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；2% 1,4-dioxane, 0.1 M tris pH 8.0,15% polyethylene glycol 3,350.
|
Resolution 2.99 Å R-free 0.248 |
| 7E3K Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants Deposited 2021-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7E3L Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants Deposited 2021-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7E3O Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody nCoV617 Deposited 2021-02-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
337–527（191 aa）
Fragment：UNP residues 337-527
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289.15 K；152 mM NH4Cl, 22.8% PEG8000
|
Resolution 2.51 Å R-free 0.259 |
| 7E5O Crystal structure of SARS-CoV-2 RBD in complex with antibody NT-193 Deposited 2021-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
322–536（215 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES pH 7.5, 10% (w/v) PEG 8000, 8% (w/v) Ethylene glycol
|
Resolution 2.80 Å R-free 0.256 |
| 7E5R SARS-CoV-2 S trimer with three-antibody cocktail complex Deposited 2021-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 21-meric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7E5S SARS-CoV-2 S trimer with four-antibody cocktail complex Deposited 2021-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7E5Y Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD Deposited 2021-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M ammonium sulfate, 12% w/v PEG 8000, and 0.1 M Tris-HCl, pH 8.5
|
Resolution 3.59 Å R-free 0.277 |
| 7E5Y Molecular basis for neutralizing antibody 2B11 targeting SARS-CoV-2 RBD Deposited 2021-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M ammonium sulfate, 12% w/v PEG 8000, and 0.1 M Tris-HCl, pH 8.5
|
Resolution 3.59 Å R-free 0.277 |
| 7E7B Cryo-EM structure of the SARS-CoV-2 furin site mutant S-Trimer from a subunit vaccine candidate Deposited 2021-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Mutation：R685A Mutation：R685A Mutation：R685A | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELA Elaidic acid × 3 VCG 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blot time 2 seconds, blot force 4, waiting time 8 seconds
|
Resolution 2.60 Å |
| 7E7D Cryo-EM structure of the SARS-CoV-2 wild-type S-Trimer from a subunit vaccine candidate Deposited 2021-02-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 ELA Elaidic acid × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blot time 2 seconds, blot force 4, waiting time 8 seconds
|
Resolution 3.20 Å |
| 7E7X SARS-CoV-2 Spike Protein N terminal domain in Complex with N11 Fab Deposited 2021-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
13–303（291 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2 M Magnesium chloride, 0.1 M Tris, pH 7.0, and 10% (w/v) polyethylene glycol 8000
|
Resolution 2.78 Å R-free 0.279 |
| 7E7X SARS-CoV-2 Spike Protein N terminal domain in Complex with N11 Fab Deposited 2021-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
13–303（291 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2 M Magnesium chloride, 0.1 M Tris, pH 7.0, and 10% (w/v) polyethylene glycol 8000
|
Resolution 2.78 Å R-free 0.279 |
| 7E7Y Crystal structure of the SARS-CoV-2 S RBD in complex with BD-623 Fab Deposited 2021-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, and 18% (w/v) polyethylene glycol 8000
|
Resolution 2.41 Å R-free 0.241 |
| 7E7Y Crystal structure of the SARS-CoV-2 S RBD in complex with BD-623 Fab Deposited 2021-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, and 18% (w/v) polyethylene glycol 8000
|
Resolution 2.41 Å R-free 0.241 |
| 7E86 Crystal structure of the SARS-CoV-2 S RBD in complex with BD-508 Fab Deposited 2021-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium citrate pH 5.0, and 11% (w/v) polyethylene glycol 6000
|
Resolution 2.90 Å R-free 0.255 |
| 7E88 Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab Deposited 2021-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.3 M Ammonium sulfate, 0.1 M Potassium sodium tartrate tetrahydrate, and 25% (w/v) polyethylene glycol 4000
|
Resolution 3.14 Å R-free 0.255 |
| 7E88 Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab Deposited 2021-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.3 M Ammonium sulfate, 0.1 M Potassium sodium tartrate tetrahydrate, and 25% (w/v) polyethylene glycol 4000
|
Resolution 3.14 Å R-free 0.255 |
| 7E88 Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab Deposited 2021-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.3 M Ammonium sulfate, 0.1 M Potassium sodium tartrate tetrahydrate, and 25% (w/v) polyethylene glycol 4000
|
Resolution 3.14 Å R-free 0.255 |
| 7E88 Crystal structure of the SARS-CoV-2 S RBD in complex with BD-515 Fab Deposited 2021-03-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: trimeric |
Chain L
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.3 M Ammonium sulfate, 0.1 M Potassium sodium tartrate tetrahydrate, and 25% (w/v) polyethylene glycol 4000
|
Resolution 3.14 Å R-free 0.255 |
| 7E8C SARS-CoV-2 S-6P in complex with 9 Fabs Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 7E8F SARS-CoV-2 NTD in complex with N9 Fab Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
13–303（291 aa）
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 7E8M Crystal structure of SARS-CoV-2 antibody P2C-1F11 with mutated RBD Deposited 2021-03-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–527（195 aa）
|
Mutation：K417N, E484K, N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.5, 12%w/v PEG 8000
|
Resolution 2.09 Å R-free 0.199 |
| 7E9N Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(1 down RBD, state1) Deposited 2021-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 7E9O Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(3 up RBDs, state2) Deposited 2021-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 7E9P Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(state2, local refinement of the RBD and 35B5 Fab) Deposited 2021-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 7E9Q Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab(1 out RBD, state3) Deposited 2021-03-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.65 Å |
| 7E9T Nanometer resolution in situ structure of SARS-CoV-2 post-fusion spike Deposited 2021-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
703–1234（532 aa）
Chain B
703–1234（532 aa）
Chain C
703–1234（532 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 10.90 Å |
| 7EAM immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6 Deposited 2021-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
Fragment：UNP residues 319-541
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293.15 K；PEG D5, 0.2M Potassium dihydrogen phosphate, 20% PEG3350
|
Resolution 1.40 Å R-free 0.181 |
| 7EAM immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 7D6 Deposited 2021-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
Fragment：UNP residues 319-541
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293.15 K；PEG D5, 0.2M Potassium dihydrogen phosphate, 20% PEG3350
|
Resolution 1.40 Å R-free 0.181 |
| 7EAN immune complex of SARS-CoV-2 RBD and cross-neutralizing antibody 6D6 Deposited 2021-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；293.15 K；0.2M sodium sulfocyanate, 20%PEG3350
|
Resolution 1.91 Å R-free 0.224 |
| 7EAZ Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 1 Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.50 Å |
| 7EB0 Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 2 Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.60 Å |
| 7EB3 Cryo-EM structure of SARS-CoV-2 Spike D614G variant, one RBD-up conformation 3 Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.60 Å |
| 7EB4 Cryo-EM structure of SARS-CoV-2 Spike D614G variant, two RBD-up conformation 1 Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.50 Å |
| 7EB5 Cryo-EM structure of SARS-CoV-2 Spike D614G variant, two RBD-up conformation 2 Deposited 2021-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.40 Å |
| 7EDF Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 1 Deposited 2021-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.20 Å |
| 7EDG Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 2 Deposited 2021-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.20 Å |
| 7EDH Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), one RBD-up conformation 3 Deposited 2021-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.60 Å |
| 7EDI Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7), two RBD-up conformation Deposited 2021-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7EDJ Cryo-EM structure of SARS-CoV-2 S-UK variant (B.1.1.7) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain Deposited 2021-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7EFP Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (S19W,N330Y) Deposited 2021-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
320–537（218 aa）
Fragment：UNP 320-537
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；1.6 M Ammonium sulfate, 0.1 M MES pH6.5, 10 % v/v 1,4-Dioxane
|
Resolution 2.70 Å R-free 0.224 |
| 7EFR Structure of SARS-CoV-2 spike receptor-binding domain in complex with high affinity ACE2 mutant (T27W,N330Y) Deposited 2021-03-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
321–537（217 aa）
Fragment：UNP residues 321-537
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；2.0 M Ammonium sulfate, 0.1 M Sodium HEPES pH7.5 , 2 % v/v PEG 400
|
Resolution 2.49 Å R-free 0.229 |
| 7EH5 Cryo-EM structure of SARS-CoV-2 S-D614G variant in complex with neutralizing antibodies, RBD-chAb15 and RBD-chAb45 Deposited 2021-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 4.00 Å |
| 7EJ4 Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-25 Deposited 2021-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.60 Å |
| 7EJ5 Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45 Deposited 2021-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.50 Å |
| 7EJY Complex Structure of antibody BD-503 and RBD of COVID-19 Deposited 2021-04-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
Fragment：Receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.15M Ammonium sulfate, 0.1M Tris, pH 8.0, 15% (w/v) PEG 400
|
Resolution 3.04 Å R-free 0.254 |
| 7EJZ Complex Structure of antibody BD-503 and RBD-S477N of COVID-19 Deposited 2021-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
Fragment：Receptor binding domain
|
Mutation：S477N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Magnesium chloride hexahydrate, 0.1M Sodium citrate, pH 5.0, 15% (w/v) PEG 4000
|
Resolution 3.63 Å R-free 0.284 |
| 7EK0 Complex Structure of antibody BD-503 and RBD-N501Y of COVID-19 Deposited 2021-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
Fragment：Receptor binding domain
|
Mutation：N501Y | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Sodium citrate, pH 5.5, 15% (w/v) PEG 6000
|
Resolution 2.70 Å R-free 0.266 |
| 7EK6 Structure of viral peptides IPB19/N52 Deposited 2021-04-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
906–957（52 aa）
Chain B
1175–1211（37 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；296 K；1.26M Sodium phosphate monobasic monohydrate, 0.14M Potassium phosphate dibasic, pH 5.6
|
Resolution 1.24 Å R-free 0.185 |
| 7EKC Structure of SARS-CoV-2 Gamma variant spike receptor-binding domain complexed with human ACE2 Deposited 2021-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Mutation：K417T, E484K, N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M MES, pH 6.5, 12% w/v PEG 20000
|
Resolution 2.80 Å R-free 0.225 |
| 7EKE Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed with human ACE2 Deposited 2021-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Mutation：F486L | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M MES, pH 6.5, 10% w/v PEG 5000 MME, 12% v/v1-Propanol
|
Resolution 2.70 Å R-free 0.241 |
| 7EKF Structure of SARS-CoV-2 Alpha variant spike receptor-binding domain complexed with human ACE2 Deposited 2021-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M MES, pH 6.5, 10% w/v PEG 5000 MME, 12% v/v1-Propanol
|
Resolution 2.85 Å R-free 0.224 |
| 7EKG Structure of SARS-CoV-2 Beta variant spike receptor-binding domain complexed with human ACE2 Deposited 2021-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Mutation：K417N, E484K, N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M MES, pH 6.5, 12% w/v PEG 20000
|
Resolution 2.63 Å R-free 0.248 |
| 7EKH Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with human ACE2 Deposited 2021-04-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Mutation：Y453F | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1 M MES, pH 6.5, 10% w/v PEG 5000 MME, 12% v/v1-Propanol
|
Resolution 2.40 Å R-free 0.228 |
| 7ENF Cryo-EM structure of the SARS-CoV-2 S-6P in complex with Fab30 Deposited 2021-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain B
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain C
1–1208（1208 aa）
Fragment：UNP residues 1-1208
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.76 Å |
| 7ENG Cryo-EM structure of the SARS-CoV-2 S-6P in complex with Fab30 (local refinement of the RBD and Fab30) Deposited 2021-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
Fragment：UNP residues 1-1208
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.59 Å |
| 7EPX S protein of SARS-CoV-2 in complex with GW01 Deposited 2021-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7EY0 Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-813 Fab and BD-744 Fab Deposited 2021-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain N
1–1207（1207 aa）
Chain R
1–1207（1207 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7EY4 Local CryoEM of the SARS-CoV-2 S6PV2 in complex with BD-667 Deposited 2021-05-29 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain N
1–290（290 aa）
Chain R
1–1207（1207 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 7EY5 Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-771 Fab and BD-821 Fab Deposited 2021-05-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
|
Resolution 3.40 Å |
| 7EYA Local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-804 Fab Deposited 2021-05-30 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain N
1–290（290 aa）
Chain R
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.77 Å |
| 7EZV local CryoEM structure of the SARS-CoV-2 S6PV2 in complex with BD-812 Fab and BD-836 Fab Deposited 2021-06-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7F0X A SARS-CoV-2 neutralizing antibody Deposited 2021-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；298 K；0.2M Potassium phosphate monobasic pH4.8, 20% w/v Polyethylene glycol 3350
|
Resolution 2.80 Å R-free 0.270 |
| 7F12 A SARS-CoV-2 neutralizing antibody Deposited 2021-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–528（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；298 K；0.2M Sodium phosphate monobasic monohydrate pH 4.7, 20% w/v Polyethylene glycol 3350
|
Resolution 3.15 Å R-free 0.245 |
| 7F15 A SARS-CoV-2 neutralizing antibody Deposited 2021-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
334–530（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；298 K；0.1M Sodium malonate pH 4.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.65 Å R-free 0.245 |
| 7F3Q SARS-CoV-2 RBD in complex with A5-10 Fab and A34-2 Fab Deposited 2021-06-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7F46 Cryo-EM structure of the SARS-CoV-2 S-6P in complex with 35B5 Fab (state1, local refinement of the RBD, NTD and 35B5 Fab) Deposited 2021-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1208（1208 aa）
Fragment：UNP residues 1-1208
Chain C
1–1208（1208 aa）
Fragment：UNP residues 1-1208
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.79 Å |
| 7F5G The crystal structure of RBD-Nanobody complex, DL4 (SA4) Deposited 2021-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
330–531（202 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 8 ACT ACETATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6 and 25% w/v Polyethylene glycol 4,000
|
Resolution 1.75 Å R-free 0.217 |
| 7F5G The crystal structure of RBD-Nanobody complex, DL4 (SA4) Deposited 2021-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
330–531（202 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 7 ACT ACETATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate pH 4.6 and 25% w/v Polyethylene glycol 4,000
|
Resolution 1.75 Å R-free 0.217 |
| 7F5H The crystal structure of RBD-Nanobody complex, DL28 (SC4) Deposited 2021-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
330–531（202 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Potassium phosphate dibasic, 20% PEG3350
|
Resolution 3.00 Å R-free 0.248 |
| 7F5H The crystal structure of RBD-Nanobody complex, DL28 (SC4) Deposited 2021-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–531（202 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Potassium phosphate dibasic, 20% PEG3350
|
Resolution 3.00 Å R-free 0.248 |
| 7F5R Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2 Deposited 2021-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；1.6M sodium/potassium phosphate
|
Resolution 3.01 Å R-free 0.218 |
| 7F5R Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2 Deposited 2021-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；1.6M sodium/potassium phosphate
|
Resolution 3.01 Å R-free 0.218 |
| 7F5R Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2 Deposited 2021-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；1.6M sodium/potassium phosphate
|
Resolution 3.01 Å R-free 0.218 |
| 7F62 Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody chAb-25 (Focused refinement of S-RBD and chAb-25 region) Deposited 2021-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.60 Å |
| 7F63 Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody chAb-45 (Focused refinement of S-RBD and chAb-45 region) Deposited 2021-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.90 Å |
| 7F6Y Complex Structure of antibody BD-503 and RBD-E484K of COVID-19 Deposited 2021-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Magnesium chloride hexahydrate, 0.1M Sodium citrate, pH 5.0, 15% (w/v) PEG 4000
|
Resolution 3.00 Å R-free 0.253 |
| 7F6Z Complex Structure of antibody BD-503 and RBD-501Y.V2 of COVID-19 Deposited 2021-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Ammonium sulfate, 0.1M Tris, pH 8.5, 12% (w/v) PEG 8000
|
Resolution 3.00 Å R-free 0.254 |
| 7F7E SARS-CoV-2 S protein RBD in complex with A5-10 Fab Deposited 2021-06-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–527（195 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Tris, PEG 6000, 100mM NaCl
|
Resolution 2.49 Å R-free 0.256 |
| 7F7H SARS-CoV-2 S protein RBD in complex with A8-1 Fab Deposited 2021-06-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
334–515（182 aa）
Fragment：RBD domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Tris, PEG 6000, 100mM NaCl
|
Resolution 3.19 Å R-free 0.275 |
| 7F7H SARS-CoV-2 S protein RBD in complex with A8-1 Fab Deposited 2021-06-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
334–515（182 aa）
Fragment：RBD domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Tris, PEG 6000, 100mM NaCl
|
Resolution 3.19 Å R-free 0.275 |
| 7FAE S protein of SARS-CoV-2 in complex bound with P36-5D2(state2) Deposited 2021-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P,K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P,K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P,K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.65 Å |
| 7FAF S protein of SARS-CoV-2 in complex bound with P36-5D2 (state1) Deposited 2021-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 7FAT Structure Determination of the RBD-NB1A7 Deposited 2021-07-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–523（191 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；8% PEG6000, 0.1 M citric acid pH 3.5 and 2% ethylene glycol
|
Resolution 1.99 Å R-free 0.242 |
| 7FAU Structure Determination of the NB1B11-RBD Complex Deposited 2021-07-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–523（191 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；16% PEG3350 and 0.1 M Zinc acetate, dehydrate
|
Resolution 2.08 Å R-free 0.228 |
| 7FAU Structure Determination of the NB1B11-RBD Complex Deposited 2021-07-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–523（191 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；16% PEG3350 and 0.1 M Zinc acetate, dehydrate
|
Resolution 2.08 Å R-free 0.228 |
| 7FB0 SARS-CoV-2 spike protein in closed state Deposited 2021-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7FB1 SARS-CoV-2 spike protein in one-RBD open state Deposited 2021-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7FB3 SARS-CoV-2 spike protein in one-RBD weak state after CTSL-treatment Deposited 2021-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7FB4 SARS-CoV-2 spike protein in two-RBD weak state after CTSL-treatment Deposited 2021-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBJ Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing nanobody 17F6 Deposited 2021-07-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
332–527（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；0.22M Sodium citrate tribasic dihydrate 23% PEG 3350
|
Resolution 2.85 Å R-free 0.300 |
| 7FBK Crystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6 Deposited 2021-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–527（196 aa）
Fragment：receptor binding domain
|
Mutation：N501Y | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；70mM Citric acid, 30mM Bis-Tris propane pH 3.4, 20% PEG 3350
|
Resolution 1.90 Å R-free 0.239 |
| 7FBK Crystal structure of SARS-CoV-2 receptor binding domain N501Y mutant in complex with neutralizing nanobody 20G6 Deposited 2021-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
332–527（196 aa）
Fragment：receptor binding domain
|
Mutation：N501Y | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；293 K；70mM Citric acid, 30mM Bis-Tris propane pH 3.4, 20% PEG 3350
|
Resolution 1.90 Å R-free 0.239 |
| 7FC5 Crystal structure of SARS-CoV-2 RBD and horse ACE2 Deposited 2021-07-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–529（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M Sodium formate, 20% w/v polyethylene glycol 3350
|
Resolution 2.89 Å R-free 0.259 |
| 7FCD Structure of the SARS-CoV-2 A372T spike glycoprotein (open) Deposited 2021-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：A372T, R682G, R683S, R685S, K986P, V987P Mutation：A372T, R682G, R683S, R685S, K986P, V987P Mutation：A372T, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7FCE Structure of the SARS-CoV-2 A372T spike glycoprotein (closed) Deposited 2021-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：A372T, R682G, R683S, R685S, K986P, V987P Mutation：A372T, R682G, R683S, R685S, K986P, V987P Mutation：A372T, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7FCP Crystallographic structure of two neutralizing antibodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD) Deposited 2021-07-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
321–591（271 aa）
|
Not recorded | TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.05 M HEPES pH 7.0
20%(w/v) PEG3350
1%(w/v) Tryptone
|
Resolution 2.40 Å R-free 0.245 |
| 7FCQ Crystallographic structure of neutralizing antibody P14-44 in complex with SARS-CoV-2 spike receptor-binding Domain (RBD) Deposited 2021-07-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；0.1 M Sodium citrate pH 5.6
20%(w/v) PEG4000
20%(V/V) Isopropanol
|
Resolution 1.89 Å R-free 0.201 |
| 7FDG SARS-COV-2 Spike RBDMACSp6 binding to hACE2 Deposited 2021-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 7FDH SARS-COV-2 Spike RBDMACSp25 binding to hACE2 Deposited 2021-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Mutation：Q493H, N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 7FDI SARS-COV-2 Spike RBDMACSp36 binding to hACE2 Deposited 2021-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Mutation：K417N, Q493H, N501H | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 7FDK SARS-COV-2 Spike RBDMACSp36 binding to mACE2 Deposited 2021-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Mutation：K417N, Q493H, N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 7FEM SARS-CoV-2 B.1.1.7 S-ACE2 complex Deposited 2021-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: eicosameric |
Chain A
15–1208（1194 aa）
Chain B
15–1208（1194 aa）
Chain C
15–1208（1194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7FET SARS-CoV-2 B.1.1.7 Spike Glycoprotein trimer Deposited 2021-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–1208（1194 aa）
Chain B
15–1208（1194 aa）
Chain C
15–1208（1194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7FG2 Minor cryo-EM structure of S protein trimer of SARS-CoV2 with K-874A VHH, composite map Deposited 2021-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7FG3 Major cryo-EM structure of S protein trimer of SARS-CoV2 with K-874, composite map Deposited 2021-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7FG7 Cryo-EM structure of S protein trimer of SARS-CoV2 Deposited 2021-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 7FH0 Crystallographic structure of two neutralizing nanobodies in complex with SARS-CoV-2 spike receptor-binding Domain (RBD) Deposited 2021-07-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 3 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M (NH4)2SO4 0.1 M TRIS pH7.5 20% (w/v) PEG1500
|
Resolution 3.20 Å R-free 0.263 |
| 7FJC Crystal structure of SARS-CoV-2 Beta RBD complexed with P36-5D2 Fab Deposited 2021-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–519（187 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289.15 K；0.1M Sodium HEPES 7.5, 10% w/v PEG6000, 5% v/v MPD
|
Resolution 2.96 Å R-free 0.269 |
| 7FJN Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex with two T6 Fab Deposited 2021-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Mutation：R682G,R683S,R685S,K968P,V969P,S305T Mutation：R682G,R683S,R685S,K968P,V969P,S305T Mutation：R682G,R683S,R685S,K968P,V969P,S305T | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 7FJO Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex with three T6 Fab Deposited 2021-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 7FJS Crystal structure of T6 Fab bound to theSARS-CoV-2 RBD of B.1.351 Deposited 2021-08-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
333–527（195 aa）
Fragment：receptor binding domain
Chain E
333–527（195 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；2.0 M ammonium sulfate, 5 % v/v 2-propanol
|
Resolution 2.90 Å R-free 0.285 |
| 7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
679–685（7 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
|
Resolution 2.36 Å R-free 0.250 |
| 7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
679–685（7 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
|
Resolution 2.36 Å R-free 0.250 |
| 7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
679–685（7 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
|
Resolution 2.36 Å R-free 0.250 |
| 7JJC Crystal structure of neuropilin-1 b1 domain in complex with SARS-CoV-2 S1 C-end rule (CendR) peptide Deposited 2020-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
679–685（7 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1 M Sodium Citrate pH 5, 20% PEG 6K
|
Resolution 2.36 Å R-free 0.250 |
| 7JJI Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry) Deposited 2020-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R682Q, R683Q, R685Q, K986P, V987P Mutation：R682Q, R683Q, R685Q, K986P, V987P Mutation：R682Q, R683Q, R685Q, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 VCG 2-hydroxyethyl 2-deoxy-3,5-bis-O-(2-hydroxyethyl)-6-O-(2-{[(9E)-octadec-9-enoyl]oxy}ethyl)-alpha-L-xylo-hexofuranoside × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7JJJ Structure of SARS-CoV-2 3Q-2P full-length dimers of spike trimers Deposited 2020-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
Chain D
1–1273（1273 aa）
Chain E
1–1273（1273 aa）
Chain F
1–1273（1273 aa）
|
Mutation：R682Q, R683Q, R685Q, K986P, V987P Mutation：R682Q, R683Q, R685Q, K986P, V987P Mutation：R682Q, R683Q, R685Q, K986P, V987P Mutation：R682Q, R683Q, R685Q, K986P, V987P Mutation：R682Q, R683Q, R685Q, K986P, V987P Mutation：R682Q, R683Q, R685Q, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7JMO Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-04 Deposited 2020-08-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；8.5% isopropanol
10% ethylene glycol
15% glycerol
0.085 M HEPES pH 7.5
17% polyethylene glycol 4000
|
Resolution 2.36 Å R-free 0.238 |
| 7JMP Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-39 Deposited 2020-08-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate pH 5.6
20% isopropanol
10% ethylene glycol
20% polyethylene glycol 4000
|
Resolution 1.71 Å R-free 0.209 |
| 7JMW Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with cross-neutralizing antibody COVA1-16 Fab Deposited 2020-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.9；293.15 K；20% PEG 3350, 0.2 M Na-iodide, pH 6.9
|
Resolution 2.89 Å R-free 0.291 |
| 7JV2 SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody Fab fragment (local refinement of the receptor-binding motif and Fab variable domains) Deposited 2020-08-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7JV4 SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody (one RBD open) Deposited 2020-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7JV6 SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody (closed conformation) Deposited 2020-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain E
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7JVA SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment (local refinement of the receptor-binding domain and Fab variable domains) Deposited 2020-08-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7JVB Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20 Deposited 2020-08-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–541（223 aa）
|
Not recorded | CAC CACODYLATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；100 mM sodium cacodylate pH 6.5, 1 M sodium citrate
|
Resolution 3.29 Å R-free 0.322 |
| 7JVB Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with nanobody Nb20 Deposited 2020-08-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | CAC CACODYLATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；100 mM sodium cacodylate pH 6.5, 1 M sodium citrate
|
Resolution 3.29 Å R-free 0.322 |
| 7JVC SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment Deposited 2020-08-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain E
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7JW0 SARS-CoV-2 spike in complex with the S304 neutralizing antibody Fab fragment Deposited 2020-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain E
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7JWB SARS CoV2 Spike ectodomain with engineered trimerized VH binder Deposited 2020-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G,R683S,R685S,R986P,V987P Mutation：R682G,R683S,R685S,R986P,V987P Mutation：R682G,R683S,R685S,R986P,V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM HEPES, pH 8, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution not provided |
| 7JWY Structure of SARS-CoV-2 spike at pH 4.5 Deposited 2020-08-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7JX3 Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology Deposited 2020-08-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain R
328–531（204 aa）
Fragment：Receptor binding domain (UNP residues 328-531)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；16.2% w/v PEG4000, 0.09 M sodium citrate, pH 6.0, 0.18 M ammonium acetate, 0.02 M potassium acetate, 0.01 MES, pH 6, 1.5% v/v pentaerythritol ethoxylate (15/4 EO/OH)
|
Resolution 2.65 Å R-free 0.288 |
| 7JZL SARS-CoV-2 spike in complex with LCB1 (2RBDs open) Deposited 2020-09-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7JZM SARS-CoV-2 spike in complex with LCB3 (local refinement of the RBD and LCB3) Deposited 2020-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7JZN SARS-CoV-2 spike in complex with LCB3 (2RBDs open) Deposited 2020-09-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7JZU SARS-CoV-2 spike in complex with LCB1 (local refinement of the RBD and LCB1) Deposited 2020-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7K43 SARS-CoV-2 spike in complex with the S2M11 neutralizing antibody Fab fragment Deposited 2020-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain E
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7K45 SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment (local refinement of the RBD and Fab variable domains) Deposited 2020-09-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7K4N SARS-CoV-2 spike in complex with the S2E12 neutralizing antibody Fab fragment Deposited 2020-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7K8M Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C102 Deposited 2020-09-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
331–517（187 aa）
Fragment：receptor binding domain (UNP residues 331-517)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M sodium citrate tribasic, 20% w/v PEG3350
|
Resolution 3.20 Å R-free 0.234 |
| 7K8S Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C002 (state 1) Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.40 Å |
| 7K8T Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C002 (State 2) Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.40 Å |
| 7K8U Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C104 Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.80 Å |
| 7K8V Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C110 Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot
|
Resolution 3.80 Å |
| 7K8W Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C119 Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain G
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.60 Å |
| 7K8X Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (State 1) Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot
|
Resolution 3.90 Å |
| 7K8Y Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C121 (State 2) Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
1–1213（1213 aa）
Chain D
1–1213（1213 aa）
Chain E
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot
|
Resolution 4.40 Å |
| 7K8Z Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C135 Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.50 Å |
| 7K90 Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, C144 Deposited 2020-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot
|
Resolution 3.24 Å |
| 7K9H SARS-CoV-2 Spike in complex with neutralizing Fab 2B04 (one up, two down conformation) Deposited 2020-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：R685A, R686*, A687*, R688*, K989P, V990P Mutation：R685A, R686*, A687*, R688*, K989P, V990P Mutation：R685A, R686*, A687*, R688*, K989P, V990P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；20s wait time
2s blot time
cryo-EM vitrification conditions
Cryogen ETHANE；20s wait time
2s blot time
|
Resolution 3.20 Å |
| 7K9I SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2B04 (local refinement) Deposited 2020-09-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
Fragment：receptor binding domain (UNP residues 333-527)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7K9J SARS-CoV-2 Spike in complex with neutralizing Fab 2H04 (three down conformation) Deposited 2020-09-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：R685A, R686*, A687*, R688*, K989P, V990P Mutation：R685A, R686*, A687*, R688*, K989P, V990P Mutation：R685A, R686*, A687*, R688*, K989P, V990P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7K9K SARS-CoV-2 Spike RBD in complex with neutralizing Fab 2H04 (local refinement) Deposited 2020-09-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
Fragment：receptor binding domain (UNP residues 333-527)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；20s wait time
2s blot time
cryo-EM vitrification conditions
Cryogen ETHANE；20s wait time
2s blot time
|
Resolution 3.14 Å |
| 7K9Z Crystal structure of SARS-CoV-2 receptor binding domain in complex with the Fab fragments of neutralizing antibodies 298 and 52 Deposited 2020-09-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；20% (w/v) 2-propanol, 20% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.6
|
Resolution 2.95 Å R-free 0.287 |
| 7KDG SARS-CoV-2 RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS) Deposited 2020-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：ectodomain
Chain B
1–1208（1208 aa）
Fragment：ectodomain
Chain C
1–1208（1208 aa）
Fragment：ectodomain
|
Mutation：R682G, R683S, R685S Mutation：R682G, R683S, R685S Mutation：R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 7KDH SARS-CoV-2 RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS) Deposited 2020-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：ectodomain
Chain B
1–1208（1208 aa）
Fragment：ectodomain
Chain C
1–1208（1208 aa）
Fragment：ectodomain
|
Mutation：R682G R683S R685S Mutation：R682G R683S R685S Mutation：R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 58 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 7KDI SARS-CoV-2 D614G 3 RBD down Spike Protein Trimer fully cleaved by furin without the P986-P987 stabilizing mutations (S-RRAR-D614G) Deposited 2020-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：ectodomain
Chain B
1–1208（1208 aa）
Fragment：ectodomain
Chain C
1–1208（1208 aa）
Fragment：ectodomain
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.26 Å |
| 7KDJ SARS-CoV-2 D614G 1-RBD-up Spike Protein Trimer fully cleaved by furin without the P986-P987 stabilizing mutations (S-RRAR-D614G) Deposited 2020-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：ectodomain
Chain B
1–1208（1208 aa）
Fragment：ectodomain
Chain C
1–1208（1208 aa）
Fragment：ectodomain
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 7KDK SARS-CoV-2 D614G 3 RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G) Deposited 2020-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：ectodomain
Chain B
1–1208（1208 aa）
Fragment：ectodomain
Chain C
1–1208（1208 aa）
Fragment：ectodomain
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7KDL SARS-CoV-2 D614G 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G) Deposited 2020-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：ectodomain
Chain B
1–1208（1208 aa）
Fragment：ectodomain
Chain C
1–1208（1208 aa）
Fragment：ectodomain
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 7KE4 SARS-CoV-2 D614G 3 RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G Sub-class) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 7KE6 SARS-CoV-2 D614G 3 RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G sub-classification) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7KE7 SARS-CoV-2 D614G 3-RBD-down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G Sub-Classification) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 7KE8 SARS-CoV-2 D614G 3 RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G sub-classification) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.26 Å |
| 7KE9 SARS-CoV-2 D614G 1-RBD-up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G sub-classification) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å |
| 7KEA SARS-CoV-2 D614G 1-RBD-up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G sub classification) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 7KEB SARS-CoV-2 D614G 1RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G sub-classification) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 7KEC SARS-CoV-2 D614G 1-RBD-up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-D614G Sub-Classification) Deposited 2020-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S Mutation：D614G R682G R683S R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
| 7KFV Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.1 M BICINE pH 8.5, 20% (w/v ) PEG 10000
|
Resolution 2.10 Å R-free 0.215 |
| 7KFV Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.1 M BICINE pH 8.5, 20% (w/v ) PEG 10000
|
Resolution 2.10 Å R-free 0.215 |
| 7KFV Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B12 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.1 M BICINE pH 8.5, 20% (w/v ) PEG 10000
|
Resolution 2.10 Å R-free 0.215 |
| 7KFW Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.2 M Ammonium phosphate dibasic, 20% w/v PEG 3350
|
Resolution 2.79 Å R-free 0.229 |
| 7KFW Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.2 M Ammonium phosphate dibasic, 20% w/v PEG 3350
|
Resolution 2.79 Å R-free 0.229 |
| 7KFW Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-B3 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.2 M Ammonium phosphate dibasic, 20% w/v PEG 3350
|
Resolution 2.79 Å R-free 0.229 |
| 7KFX Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-C2 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl pH 7.5
mother liquor composition (equal volume): 0.03 M Citric acid, 0.07M BIS-TRIS propane/pH 7.6, 20% (w/v) PEG 3350
|
Resolution 2.23 Å R-free 0.226 |
| 7KFY Structural basis for a germline-biased antibody response to SARS-CoV-2 (RBD:C1A-F10 Fab) Deposited 2020-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；protein sample: 13 mg/mL in 150mM NaCl, 25 mM Tris-HCl, pH 7.5
mother liquor composition (equal volume): 0.10% (w/v) n-Octyl-B-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 4.5, 22% (w/v) PEG 3350
|
Resolution 2.16 Å R-free 0.249 |
| 7KGJ Crystal structure of synthetic nanobody (Sb45) complexes with SARS-CoV-2 receptor binding domain Deposited 2020-10-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；12% PEG 8000, 0.1M Hepes pH 7.5, 0.2M NaCl
|
Resolution 2.30 Å R-free 0.216 |
| 7KGK Crystal structure of synthetic nanobody (Sb16) complexes with SARS-CoV-2 receptor binding domain Deposited 2020-10-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–527（195 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；15% PEG 20000, and 0.1M Hepes pH 7.0
|
Resolution 2.60 Å R-free 0.276 |
| 7KJ2 SARS-CoV-2 Spike Glycoprotein with one ACE2 Bound Deposited 2020-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7KJ3 SARS-CoV-2 Spike Glycoprotein with two ACE2 Bound Deposited 2020-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 40 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7KJ4 SARS-CoV-2 Spike Glycoprotein with three ACE2 Bound Deposited 2020-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7KJ5 SARS-CoV-2 Spike Glycoprotein, prefusion with one RBD up conformation Deposited 2020-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7KKK SARS-CoV-2 Spike in complex with neutralizing nanobody Nb6 Deposited 2020-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 7KKL SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 Deposited 2020-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 7KL9 Structure of the SARS-CoV-2 S 6P trimer in complex with the ACE2 protein decoy, CTC-445.2 (State 4) Deposited 2020-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 4.10 Å |
| 7KLG SARS-CoV-2 RBD in complex with Fab 15033 Deposited 2020-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–528（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.4 M (NH4)2SO4, 10% 1,2-propanediol
|
Resolution 3.20 Å R-free 0.290 |
| 7KLG SARS-CoV-2 RBD in complex with Fab 15033 Deposited 2020-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
328–528（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.4 M (NH4)2SO4, 10% 1,2-propanediol
|
Resolution 3.20 Å R-free 0.290 |
| 7KLH SARS-CoV-2 RBD in complex with Fab 15033-7 Deposited 2020-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–528（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.4 M (NH4)2SO4 16% glycerol
|
Resolution 3.00 Å R-free 0.283 |
| 7KLH SARS-CoV-2 RBD in complex with Fab 15033-7 Deposited 2020-10-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
328–528（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.4 M (NH4)2SO4 16% glycerol
|
Resolution 3.00 Å R-free 0.283 |
| 7KLW Crystal structure of synthetic nanobody (Sb45+Sb68) complexes with SARS-CoV-2 receptor binding domain Deposited 2020-11-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
Fragment：RBD domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；10% PEG 8000, 0.1M Sodium Cacodylate pH 6.0
|
Resolution 2.60 Å R-free 0.255 |
| 7KM5 Crystal structure of SARS-CoV-2 RBD complexed with Nanosota-1 Deposited 2020-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–535（217 aa）
Fragment：receptor-binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；50 mM MnCl2, 50 mM MES (pH 6.0), 20% (W/V) PEG 4000
|
Resolution 3.19 Å R-free 0.294 |
| 7KM5 Crystal structure of SARS-CoV-2 RBD complexed with Nanosota-1 Deposited 2020-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–535（217 aa）
Fragment：receptor-binding domain
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；50 mM MnCl2, 50 mM MES (pH 6.0), 20% (W/V) PEG 4000
|
Resolution 3.19 Å R-free 0.294 |
| 7KMB ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 7.4 Deposited 2020-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 7KMG LY-CoV555 neutralizing antibody against SARS-CoV-2 Deposited 2020-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
329–527（199 aa）
Fragment：receptor-binding domain
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；20% PEG 10000,
sodium acetate pH 4.6
|
Resolution 2.16 Å R-free 0.257 |
| 7KMG LY-CoV555 neutralizing antibody against SARS-CoV-2 Deposited 2020-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
329–527（199 aa）
Fragment：receptor-binding domain
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；20% PEG 10000,
sodium acetate pH 4.6
|
Resolution 2.16 Å R-free 0.257 |
| 7KMH LY-CoV488 neutralizing antibody against SARS-CoV-2 Deposited 2020-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
329–527（199 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 PRO PROLINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.7；293 K；8% PEG 3350,
200 mM L-Proline,
100 mM Hepes pH 7.7
|
Resolution 1.72 Å R-free 0.242 |
| 7KMI LY-CoV481 neutralizing antibody against SARS-CoV-2 Deposited 2020-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
329–527（199 aa）
Fragment：receptor-binding domain
|
Not recorded | GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.8；293 K；14% PEG 4000,
10% 2-Propanol,
100 mM Tri-Sodium Citrate pH 5.8
|
Resolution 1.73 Å R-free 0.217 |
| 7KMK cryo-EM structure of SARS-CoV-2 spike in complex with Fab 15033-7, two RBDs bound Deposited 2020-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE；blotting force = 1
blotting time = 2.5 s
|
Resolution 4.20 Å |
| 7KML cryo-EM structure of SARS-CoV-2 spike in complex with Fab 15033-7, three RBDs bound Deposited 2020-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE；blotting force = 1
blotting time = 2.5 s
|
Resolution 3.80 Å |
| 7KMS Cryo-EM structure of triple ACE2-bound SARS-CoV-2 trimer spike at pH 7.4 Deposited 2020-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 55 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.64 Å |
| 7KMZ Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4 Deposited 2020-11-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 53 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 7KN3 Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-B8 Fab Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 2 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；20% PEG 3350, 0.2 M sodium sulfate, pH 6.6
|
Resolution 2.25 Å R-free 0.222 |
| 7KN3 Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-B8 Fab Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.6；293 K；20% PEG 3350, 0.2 M sodium sulfate, pH 6.6
|
Resolution 2.25 Å R-free 0.222 |
| 7KN4 Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-E6 Fab Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% isopropanol, 20% PEG 4000, 0.1 M citrate pH 5.6
|
Resolution 2.70 Å R-free 0.291 |
| 7KN4 Crystal structure of SARS-CoV-2 spike protein receptor-binding domain complexed with a pre-pandemic antibody S-E6 Fab Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% isopropanol, 20% PEG 4000, 0.1 M citrate pH 5.6
|
Resolution 2.70 Å R-free 0.291 |
| 7KN5 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG-3000, 0.1 M citrate pH 5.5
|
Resolution 1.87 Å R-free 0.213 |
| 7KN5 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG-3000, 0.1 M citrate pH 5.5
|
Resolution 1.87 Å R-free 0.213 |
| 7KN6 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3 Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2 M Na2HPO4, pH 9.1
|
Resolution 2.55 Å R-free 0.238 |
| 7KN7 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3 Deposited 2020-11-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.0 M Li-chloride, 10% PEG-6000, 0.1 M Bicine pH 9.0
|
Resolution 2.73 Å R-free 0.241 |
| 7KNB Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 7.4 Deposited 2020-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 46 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.93 Å |
| 7KNE Cryo-EM structure of single ACE2-bound SARS-CoV-2 trimer spike at pH 5.5 Deposited 2020-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 44 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5；PBS with NaAcetate pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 7KNH Cryo-EM Structure of Double ACE2-Bound SARS-CoV-2 Trimer Spike at pH 5.5 Deposited 2020-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5；PBS with NaAcetate pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.74 Å |
| 7KNI Cryo-EM structure of Triple ACE2-bound SARS-CoV-2 Trimer Spike at pH 5.5 Deposited 2020-11-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 56 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5；PBS with NaAcetate pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.91 Å |
| 7KQB SARS-CoV-2 spike glycoprotein:Fab 5A6 complex I Deposited 2020-11-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；8-10 seconds, blot force 0
|
Resolution 2.42 Å |
| 7KQE SARS-CoV-2 spike glycoprotein:Fab 3D11 complex Deposited 2020-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；8-10 seconds, blot force 0
|
Resolution 2.88 Å |
| 7KRQ Structural impact on SARS-CoV-2 spike protein by D614G substitution Deposited 2020-11-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å R-free 0.425 |
| 7KRR Structural impact on SARS-CoV-2 spike protein by D614G substitution Deposited 2020-11-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å R-free 0.437 |
| 7KRS Structural impact on SARS-CoV-2 spike protein by D614G substitution Deposited 2020-11-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å R-free 0.479 |
| 7KS9 Cryo-EM structure of prefusion SARS-CoV-2 spike glycoprotein in complex with 910-30 Fab Deposited 2020-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.75 Å |
| 7KSG SARS-CoV-2 spike in complex with nanobodies E Deposited 2020-11-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 7KXJ SARS-CoV-2 spike protein in complex with Fab 15033-7, 3-"up", asymmetric Deposited 2020-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE；blotting force = 1
blotting time = 2.5 s
|
Resolution 6.40 Å |
| 7KXK SARS-CoV-2 spike protein in complex with Fab 15033-7, 2-"up"-1-"down" conformation Deposited 2020-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE；blotting force = 1
blotting time = 2.5 s
|
Resolution 5.00 Å |
| 7KZB Potent SARS-CoV-2 binding and neutralization through maturation of iconic SARS-CoV-1antibodies Deposited 2020-12-10 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
333–528（196 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；200 mM NaCl, 100 mM Tris (pH 8.0), 20% (w/v) PEG3350
|
Resolution 2.83 Å R-free 0.336 |
| 7L02 Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound to one copy of domain-swapped antibody 2G12 Deposited 2020-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7L06 Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound to two copies of domain-swapped antibody 2G12 Deposited 2020-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7L09 Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound domain-swapped antibody 2G12 from masked 3D refinement Deposited 2020-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7L0N Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity Deposited 2020-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain R
328–531（204 aa）
Fragment：Binding domain
|
Not recorded | CL CHLORIDE ION × 8 SO4 SULFATE ION × 1 NA SODIUM ION × 4 PG5 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.09 M Buffer System 3 pH 8.5 contains Tris (base); BICINE
27% Precipitant Mix 2 contains Ethylene glycol and PEG8000
0.1 M Ammonium sulfate
|
Resolution 2.78 Å R-free 0.325 |
| 7L0N Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity Deposited 2020-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain S
328–531（204 aa）
Fragment：Binding domain
|
Not recorded | CL CHLORIDE ION × 19 SO4 SULFATE ION × 1 NA SODIUM ION × 2 PG4 TETRAETHYLENE GLYCOL × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.09 M Buffer System 3 pH 8.5 contains Tris (base); BICINE
27% Precipitant Mix 2 contains Ethylene glycol and PEG8000
0.1 M Ammonium sulfate
|
Resolution 2.78 Å R-free 0.325 |
| 7L2C Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD) Deposited 2020-12-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–334（334 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CA CALCIUM ION × 23 ACT ACETATE ION × 3 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.16 M Calcium Acetate, 0.08 M Sodium Cacodylate, 14.4% PEG 8000, 20% Glycerol
|
Resolution 3.65 Å R-free 0.272 |
| 7L2C Crystallographic structure of neutralizing antibody 2-51 in complex with SARS-CoV-2 spike N-terminal domain (NTD) Deposited 2020-12-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–334（334 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 CA CALCIUM ION × 16 ACT ACETATE ION × 6 CAC CACODYLATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.16 M Calcium Acetate, 0.08 M Sodium Cacodylate, 14.4% PEG 8000, 20% Glycerol
|
Resolution 3.65 Å R-free 0.272 |
| 7L2D Cryo-EM structure of NTD-directed neutralizing antibody 1-87 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2020-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 7L2E Cryo-EM structure of NTD-directed neutralizing antibody 4-18 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2020-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |
| 7L2F Cryo-EM structure of NTD-directed neutralizing antibody 5-24 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2020-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7L3N SARS-CoV 2 Spike Protein bound to LY-CoV555 Deposited 2020-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
13–1208（1196 aa）
Chain B
13–1208（1196 aa）
Chain C
13–1208（1196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 7L4Z Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide Deposited 2020-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；200 mM ammonium sulfate, 24% PEG 4000, 12% glycerol
|
Resolution 3.96 Å R-free 0.282 |
| 7L4Z Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide Deposited 2020-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
319–541（223 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；200 mM ammonium sulfate, 24% PEG 4000, 12% glycerol
|
Resolution 3.96 Å R-free 0.282 |
| 7L4Z Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide Deposited 2020-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–541（223 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；200 mM ammonium sulfate, 24% PEG 4000, 12% glycerol
|
Resolution 3.96 Å R-free 0.282 |
| 7L4Z Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide Deposited 2020-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
319–541（223 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；200 mM ammonium sulfate, 24% PEG 4000, 12% glycerol
|
Resolution 3.96 Å R-free 0.282 |
| 7L4Z Structure of SARS-CoV-2 spike RBD in complex with cyclic peptide Deposited 2020-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–541（223 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；200 mM ammonium sulfate, 24% PEG 4000, 12% glycerol
|
Resolution 3.96 Å R-free 0.282 |
| 7L56 Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-43 Deposited 2020-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7L57 Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-15 Deposited 2020-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.87 Å |
| 7L58 Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab H4 Deposited 2020-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S Mutation：K986P, V987P, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.07 Å |
| 7L5B Crystallographic structure of neutralizing antibody 2-15 in complex with SARS-CoV-2 spike receptor-binding Domain (RBD). Deposited 2020-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1 M Hepes, 70 % MPD
|
Resolution 3.18 Å R-free 0.239 |
| 7L7D Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibody AZD8895 Deposited 2020-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–529（200 aa）
Fragment：receptor binding domain (UNP residues 330-529)
|
Not recorded | GOL GLYCEROL × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；16% PEG3350, 0.2 M Tris-HCl, pH 8.5
|
Resolution 2.50 Å R-free 0.231 |
| 7L7E Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibodies AZD8895 and AZD1061 Deposited 2020-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
330–529（200 aa）
Fragment：receptor binding domain (UNP residues 330-529)
|
Not recorded | PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；5% PEG1000, 40% reagent alcohol, 0.1 M sodium phosphate dibasic/citric acid, pH 4.2
|
Resolution 3.00 Å R-free 0.273 |
| 7L7E Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibodies AZD8895 and AZD1061 Deposited 2020-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain b
330–529（200 aa）
Fragment：receptor binding domain (UNP residues 330-529)
|
Not recorded | PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；5% PEG1000, 40% reagent alcohol, 0.1 M sodium phosphate dibasic/citric acid, pH 4.2
|
Resolution 3.00 Å R-free 0.273 |
| 7L7E Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibodies AZD8895 and AZD1061 Deposited 2020-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain S
330–529（200 aa）
Fragment：receptor binding domain (UNP residues 330-529)
|
Not recorded | PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；5% PEG1000, 40% reagent alcohol, 0.1 M sodium phosphate dibasic/citric acid, pH 4.2
|
Resolution 3.00 Å R-free 0.273 |
| 7L7E Crystal structure of SARS-CoV-2 spike RBD in complex with human monoclonal antibodies AZD8895 and AZD1061 Deposited 2020-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain K
330–529（200 aa）
Fragment：receptor binding domain (UNP residues 330-529)
|
Not recorded | PO4 PHOSPHATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；5% PEG1000, 40% reagent alcohol, 0.1 M sodium phosphate dibasic/citric acid, pH 4.2
|
Resolution 3.00 Å R-free 0.273 |
| 7L7F Cryo-EM structure of human ACE2 receptor bound to protein encoded by vaccine candidate BNT162b1 Deposited 2020-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
1–16（16 aa）
Chain E
327–528（202 aa）
Chain F
1–16（16 aa）
Chain F
327–528（202 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.24 Å |
| 7L7K Cryo-EM structure of protein encoded by vaccine candidate BNT162b2 Deposited 2020-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 7LAA Structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1041 Deposited 2021-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7LAB Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1052 Deposited 2021-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |
| 7LC8 SARS-CoV-2 spike Protein TM domain Deposited 2021-01-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1217–1237（21 aa）
Fragment：TM domain, residues 1217-1237
Chain B
1217–1237（21 aa）
Fragment：TM domain, residues 1217-1237
Chain C
1217–1237（21 aa）
Fragment：TM domain, residues 1217-1237
|
Mutation：M1229L, M1233L Mutation：M1229L, M1233L Mutation：M1229L, M1233L | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；303 K；Ionic strength (raw mmCIF value) 20；Pressure 1
NMR sample composition
55 mM [U-99% 2H] 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM [U-99% 2H] 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-13C; U-15N] Spike glycoprotein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
55 mM [U-99% 2H] 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM [U-99% 2H] 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-13C; U-15N; U-2H] Spike glycoprotein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
55 mM 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-15N; U-2H] Spike glycoprotein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
55 mM 1,2-dimyristoyl-sn-Glycero-3-Phosphocholine, 100 mM 1,2-dihexanoyl-sn-Glycero-3-Phosphocholine, 20 mM TRIS, 0.02 % sodium azide, 20 mM sodium chloride, 1 mM [U-13C; U-15N; U-2H] Spike glycoprotein, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 7LCN Structure of SARS-CoV-2 S protein in complex with N-terminal domain antibody DH1050.1 Deposited 2021-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
Chain K
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 7LD1 Structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1047 Deposited 2021-01-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7LDJ SARS-CoV-2 receptor binding domain in complex with WNb-2 Deposited 2021-01-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
331–527（197 aa）
Fragment：receptor binding domain (UNP residues 331-527)
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG4000, potassium thiocyanate, sodium cacodylate
|
Resolution 2.36 Å R-free 0.268 |
| 7LDJ SARS-CoV-2 receptor binding domain in complex with WNb-2 Deposited 2021-01-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain (UNP residues 331-527)
|
Not recorded | MAN alpha-D-mannopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG4000, potassium thiocyanate, sodium cacodylate
|
Resolution 2.36 Å R-free 0.268 |
| 7LDJ SARS-CoV-2 receptor binding domain in complex with WNb-2 Deposited 2021-01-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
331–527（197 aa）
Fragment：receptor binding domain (UNP residues 331-527)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG4000, potassium thiocyanate, sodium cacodylate
|
Resolution 2.36 Å R-free 0.268 |
| 7LDJ SARS-CoV-2 receptor binding domain in complex with WNb-2 Deposited 2021-01-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
331–527（197 aa）
Fragment：receptor binding domain (UNP residues 331-527)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG4000, potassium thiocyanate, sodium cacodylate
|
Resolution 2.36 Å R-free 0.268 |
| 7LJR SARS-CoV-2 Spike Protein Trimer bound to DH1043 fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 7LM8 Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with two cross-neutralizing antibodies CV38-142 and COVA1-16 Fabs isolated from COVID-19 patients Deposited 2021-02-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 16 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；293 K；10% (w/v) polyethylene glycol 6000, 0.1 M citric acid pH 4.0
|
Resolution 1.94 Å R-free 0.201 |
| 7LO4 SARS-CoV-2 spike receptor-binding domain with a G485R mutation in complex with human ACE2 Deposited 2021-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–530（198 aa）
|
Mutation：G485R | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；Protein: 5 mg/mL in 20 mM Tris pH 7.5, 150 mM NaCl
Reservoir: 0.1 M HEPES pH 7.0, 16% w/v PEG 8000
Cryobuffer: reservoir solution + 20% ethylene glycol
|
Resolution 2.46 Å R-free 0.251 |
| 7LOP Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV05-163 and CR3022 Deposited 2021-02-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain Z
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；293.15 K；0.1 M sodium citrate - citric acid buffer at pH 4.8 and 19% (w/v) polyethylene glycol 6000
|
Resolution 2.25 Å R-free 0.268 |
| 7LOP Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV05-163 and CR3022 Deposited 2021-02-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；293.15 K；0.1 M sodium citrate - citric acid buffer at pH 4.8 and 19% (w/v) polyethylene glycol 6000
|
Resolution 2.25 Å R-free 0.268 |
| 7LQ7 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies CV503 and COVA1-16 Deposited 2021-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
333–530（198 aa）
Chain B
333–530（198 aa）
Chain E
333–530（198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate pH 4.2, 1 M lithium chloride, and 9% (w/v) polyethylene glycol 6000
|
Resolution 3.40 Å R-free 0.233 |
| 7LQV Cryo-EM structure of NTD-directed neutralizing antibody 4-8 Fab in complex with SARS-CoV-2 S2P spike Deposited 2021-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 7LQW Cryo-EM structure of NTD-directed neutralizing antibody 2-17 Fab in complex with SARS-CoV-2 S2P spike Deposited 2021-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.47 Å |
| 7LRS Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain Deposited 2021-02-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
332–527（196 aa）
Fragment：receptor binding domain (UNP residues 332-527)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, pH 7.4, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 1.5 seconds before plugging.
|
Resolution 3.89 Å |
| 7LRT Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain Deposited 2021-02-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 4 seconds before plugging.
|
Resolution 3.54 Å |
| 7LS9 Cryo-EM structure of neutralizing antibody 1-57 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2021-02-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7LSS Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-7 Deposited 2021-02-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 7LWI Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 7LWJ Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.24 Å |
| 7LWK Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.92 Å |
| 7LWL Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 3-RBD down conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.84 Å |
| 7LWM Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 7LWN Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 7LWO Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 1-RBD up conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 7LWP Mink Cluster 5-associated SARS-CoV-2 spike protein (S-GSAS-D614G-delFV) in the 2-RBD up conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 7LWQ Mink Cluster 5-associated SARS-CoV-2 spike protein(S-GSAS-D614G-delFV) missing the S1 subunit and SD2 subdomain of one protomer Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S Mutation：del(H69-V70), Y453F, D614G, I692V, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 7LWS UK (B.1.1.7) SARS-CoV-2 S-GSAS-D614G variant spike protein in the 3-RBD-down conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 7LWT UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.19 Å |
| 7LWU UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 7LWV UK (B.1.1.7) SARS-CoV-2 spike protein variant (S-GSAS-B.1.1.7) in the 1-RBD-up conformation Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S Mutation：del(H69-V70), del(Y144), N501Y, A570D, D614G, P681H, T716I, S982A, D1118H, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 7LWW Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 1-RBD-up conformation (S-GSAS-D614G-K417N-E484K-N501Y) Deposited 2021-03-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7LX5 The SARS-CoV-2 spike protein receptor binding domain bound to neutralizing nanobodies WNb 2 and WNb 10 Deposited 2021-03-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 7LXW SARS-CoV-2 S/S2M11/S2X333 Local Refinement Deposited 2021-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7LXX SARS-CoV-2 S/S2M11/S2L28 Local Refinement Deposited 2021-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7LXY SARS-CoV-2 S/S2M11/S2X333 Global Refinement Deposited 2021-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain J
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å |
| 7LXZ SARS-CoV-2 S/S2M11/S2L28 Global Refinement Deposited 2021-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7LY0 SARS-CoV-2 S/S2M11/S2M28 Local Refinement Deposited 2021-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7LY2 SARS-CoV-2 S/S2M11/S2M28 Global Refinement Deposited 2021-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain J
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7LY3 Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab Deposited 2021-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–307（294 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 UNX UNKNOWN LIGAND × 1 XYL Xylitol × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.75；293 K；10 mM HEPES-HCl pH 8.0
750 mM NaCl
0.1 M Ammonium Sulfate
0.05 M Sodium Citrate pH 4.75
12.5 % PEG4000
|
Resolution 3.00 Å R-free 0.234 |
| 7LY3 Crystal structure of SARS-CoV-2 S NTD bound to S2M28 Fab Deposited 2021-03-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
14–307（294 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 UNX UNKNOWN LIGAND × 1 XYL Xylitol × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.75；293 K；10 mM HEPES-HCl pH 8.0
750 mM NaCl
0.1 M Ammonium Sulfate
0.05 M Sodium Citrate pH 4.75
12.5 % PEG4000
|
Resolution 3.00 Å R-free 0.234 |
| 7LYK South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 2-RBD-up conformation Deposited 2021-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.65 Å |
| 7LYL South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the RBD-down conformation Deposited 2021-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 7LYM South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the RBD-down conformation Deposited 2021-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.57 Å |
| 7LYN South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Deposited 2021-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 7LYO South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Deposited 2021-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 40 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 7LYP South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Deposited 2021-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.05 Å |
| 7LYQ South African (B.1.351) SARS-CoV-2 spike protein variant (S-GSAS-B.1.351) in the 1-RBD-up conformation Deposited 2021-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S Mutation：N501Y, K417N, E484K, L18F, D80A, D215G, R246I, A701V, D614G, R682G, R683S, R685S | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 7M0J SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer - asymmetric refinement Deposited 2021-03-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain B
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
Chain C
16–1208（1193 aa）
Fragment：ectodomain (UNP residues 16-1208)
|
Mutation：A570L, T572I, F855Y, N856I, K986V, V987P, R682G, R683S, R685S Mutation：A570L, T572I, F855Y, N856I, K986V, V987P, R682G, R683S, R685S Mutation：A570L, T572I, F855Y, N856I, K986V, V987P, R682G, R683S, R685S | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7M3I Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75 Fab Deposited 2021-03-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–591（273 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M Tris, pH 7.5, 0.1M Calcium acetate, 15% PEG 3350
|
Resolution 2.80 Å R-free 0.281 |
| 7M3I Structure of SARS-CoV-2 spike protein receptor binding domain in complex with a neutralizing antibody, CV2-75 Fab Deposited 2021-03-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–591（273 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M Tris, pH 7.5, 0.1M Calcium acetate, 15% PEG 3350
|
Resolution 2.80 Å R-free 0.281 |
| 7M42 Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of neutralizing antibodies REGN10985 and REGN10989 Deposited 2021-03-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
319–541（223 aa）
Fragment：receptor binding domain (UNP residues 319-541)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7M53 B6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide Deposited 2021-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1146–1161（16 aa）
Fragment：residues 1146-1161 of the spike glycoprotein
|
Not recorded | GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Potassium Chloride and 20% (w/v) PEG3350
|
Resolution 1.40 Å R-free 0.174 |
| 7M6D Structure of the SARS-CoV-2 RBD in complex with neutralizing antibodies BG4-25 and CR3022 Deposited 2021-03-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
328–533（206 aa）
Fragment：Receptor Binding Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；298 K；0.05 M citric acid, 0.05 M BIS-TRIS propane pH 5.0, 16% polyethylene glycol 3350
|
Resolution 3.10 Å R-free 0.259 |
| 7M6E Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG10-19 Deposited 2021-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.30 Å |
| 7M6F Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG1-22 Deposited 2021-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.90 Å |
| 7M6G Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG7-15 Deposited 2021-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.70 Å |
| 7M6H Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG7-20 Deposited 2021-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 4.00 Å |
| 7M6I Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG1-24 Deposited 2021-03-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 4.00 Å |
| 7M71 SARS-CoV-2 Spike:5A6 Fab complex I focused refinement Deposited 2021-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
|
Mutation：R682G,R683S,R685S,K986P,V987P Mutation：R682G,R683S,R685S,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；8-10 seconds, blot force 0
|
Resolution 2.66 Å |
| 7M7B SARS-CoV-2 Spike:Fab 3D11 complex focused refinement Deposited 2021-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G,R683S,R685S,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；8-10 seconds, blot force 0
|
Resolution 2.95 Å |
| 7M7W Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape Deposited 2021-03-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain S
328–531（204 aa）
Fragment：receptor binding domain (UNP residues 328-531)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；30% Precipitant Mix 2 (Molecular Dimensions; ethylene glycol, PEG8000), 0.1 M Buffer System 3, pH 8.5 (Molecular Dimensions; Tris (base)/BICINE), 0.12 M Monosaccharides Mix (Molecular Dimensions), 0.02 M sodium chloride, 0.01 M MES, pH 6, 3% v/v Jeffamine ED-2003
|
Resolution 2.65 Å R-free 0.271 |
| 7M7W Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape Deposited 2021-03-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
328–531（204 aa）
Fragment：receptor binding domain (UNP residues 328-531)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；30% Precipitant Mix 2 (Molecular Dimensions; ethylene glycol, PEG8000), 0.1 M Buffer System 3, pH 8.5 (Molecular Dimensions; Tris (base)/BICINE), 0.12 M Monosaccharides Mix (Molecular Dimensions), 0.02 M sodium chloride, 0.01 M MES, pH 6, 3% v/v Jeffamine ED-2003
|
Resolution 2.65 Å R-free 0.271 |
| 7M8J SARS-CoV-2 S-NTD + Fab CM25 Deposited 2021-03-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–270（257 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；-4 force, 3 s blot
|
Resolution 3.48 Å |
| 7M8K Cryo-EM structure of Brazil (P.1) SARS-CoV-2 spike glycoprotein variant in the prefusion state (1 RBD up) Deposited 2021-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7M8S Crystal Structure of HLA-A*02:01 in complex with KLNDLCFTNV, an 10-mer epitope from SARS-CoV-2 Spike (S386-395) Deposited 2021-03-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
386–395（10 aa）
Fragment：UNP residues 386-395
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.2 Ammonium tantrate, 0.001 Cadmium chloride, 14% PEG 3350
|
Resolution 2.35 Å R-free 0.247 |
| 7M8S Crystal Structure of HLA-A*02:01 in complex with KLNDLCFTNV, an 10-mer epitope from SARS-CoV-2 Spike (S386-395) Deposited 2021-03-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
386–395（10 aa）
Fragment：UNP residues 386-395
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；277 K；0.2 Ammonium tantrate, 0.001 Cadmium chloride, 14% PEG 3350
|
Resolution 2.35 Å R-free 0.247 |
| 7M8T Crystal Structure of HLA-A*11:01 in complex with NSASFSTFK, an 9-mer epitope from SARS-CoV-2 spike (S370-378) Deposited 2021-03-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
370–378（9 aa）
Fragment：UNP residues 370-378
|
Not recorded | GOL GLYCEROL × 1 SO4 SULFATE ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；2M Ammonium Sulfate, 0.1M Calcium cacodylate pH 6.5, 0.2M sodium chloride
|
Resolution 1.50 Å R-free 0.219 |
| 7M8U Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from SARS-CoV-2 spike (S896-904) Deposited 2021-03-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
896–904（9 aa）
Fragment：UNP residues 896-904
|
Not recorded | PO4 PHOSPHATE ION × 2 NA SODIUM ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.2 sodium fluoride, 18% PEG 3350
|
Resolution 1.45 Å R-free 0.229 |
| 7MDW CryoEM structure of SARS-CoV-2 RBD in complex with nanobodies Nb21 and Nb105 Deposited 2021-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 7ME7 CryoEM structure of SARS-CoV-2 RBD in complex with nanobodies Nb17 and Nb105 Deposited 2021-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.73 Å |
| 7MEJ CryoEM structure of SARS-CoV-2 RBD in complex with nanobodies Nb21 and Nb36 Deposited 2021-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 7MF1 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 47D1 Deposited 2021-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；8.5% isopropanol, 17% PEG 4000, 0.085 M HEPES pH 7.5, 15% glycerol
|
Resolution 2.09 Å R-free 0.250 |
| 7MFU Crystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain Deposited 2021-04-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–528（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 8000, 0.1M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.215 |
| 7MFU Crystal structure of synthetic nanobody (Sb14+Sb68) complexes with SARS-CoV-2 receptor binding domain Deposited 2021-04-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
332–528（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG 8000, 0.1M Hepes pH 7.5
|
Resolution 1.70 Å R-free 0.215 |
| 7MJG Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y Mutation：N501Y Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 7MJH Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8 Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y Mutation：N501Y Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 7MJI Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8 (focused refinement of RBD and VH ab8) Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 7MJJ Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 1) Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y Mutation：N501Y Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 7MJK Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 2) Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y Mutation：N501Y Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.73 Å |
| 7MJL Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (focused refinement of RBD and Fab ab1) Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 7MJM Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y Mutation：N501Y Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 7MJN Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 7MKB Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL Deposited 2021-04-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；290 K；17% PEG10000, 0.1 M Bis-Tris, pH 5.5, 0.1 M ammonium acetate
|
Resolution 1.90 Å R-free 0.209 |
| 7MKL SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-38 (three down conformation) Deposited 2021-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7MKM SARS-CoV-2 Spike RBD in complex with neutralizing Fab SARS2-38 (local refinement) Deposited 2021-04-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–520（188 aa）
Fragment：receptor binding domain (UNP residues 333-520)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 7MLZ Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody B1-182.1 that targets the receptor-binding domain Deposited 2021-04-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor binding domain, UNP residues 331-527
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 4 seconds before plugging.
|
Resolution 3.71 Å |
| 7MM0 Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody B1-182.1 that targets the receptor-binding domain Deposited 2021-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 4 seconds before plugging.
|
Resolution 3.15 Å |
| 7MMO LY-CoV1404 neutralizing antibody against SARS-CoV-2 Deposited 2021-04-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
329–527（199 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；200mM Trimethylamine N-oxide, 20% PEG MME 2K, 100mM Tris HCl pH 6.0-7.0
|
Resolution 2.43 Å R-free 0.253 |
| 7MMO LY-CoV1404 neutralizing antibody against SARS-CoV-2 Deposited 2021-04-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
329–527（199 aa）
Fragment：receptor-binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；200mM Trimethylamine N-oxide, 20% PEG MME 2K, 100mM Tris HCl pH 6.0-7.0
|
Resolution 2.43 Å R-free 0.253 |
| 7MSQ Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD) Deposited 2021-05-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | CL CHLORIDE ION × 2 SCN THIOCYANATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；Protein complex (5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 100 mM BisTrisPropane (pH 6.9), 800 mM KSCN, 10% (v/v) glycerol, and 18%(m/v) PEG8000
|
Resolution 2.29 Å R-free 0.245 |
| 7MSQ Complex between the Fab arm of AB-3467 and the SARS-CoV-2 receptor binding domain (RBD) Deposited 2021-05-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | CL CHLORIDE ION × 5 SCN THIOCYANATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.9；293 K；Protein complex (5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) was mixed with an equal volume (2 uL) of well solution comprising 100 mM BisTrisPropane (pH 6.9), 800 mM KSCN, 10% (v/v) glycerol, and 18%(m/v) PEG8000
|
Resolution 2.29 Å R-free 0.245 |
| 7MTC Structure of freshly purified SARS-CoV-2 S2P spike at pH 7.4 Deposited 2021-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7MTD Structure of aged SARS-CoV-2 S2P spike at pH 7.4 Deposited 2021-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7MTE Structure of SARS-CoV-2 S2P spike at pH 7.4 refolded by low-pH treatment Deposited 2021-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7MW2 Structure of the SARS-CoV-2 Spike trimer with all RBDs down in complex with the Fab fragment of human neutralizing antibody clone 6 Deposited 2021-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |
| 7MW3 Structure of the SARS-CoV-2 Spike trimer with two RBDs down in complex with the Fab fragment of human neutralizing antibody clone 6 Deposited 2021-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 7MW4 Structure of the SARS-CoV-2 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody clone 6 Deposited 2021-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7MW5 Structure of the SARS-CoV-2 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody clone 2 Deposited 2021-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7MW6 Structure of the SARS-CoV-2 Spike trimer with three RBDs up in complex with the Fab fragment of human neutralizing antibody clone 2 Deposited 2021-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 7MXP Cryo-EM structure of NTD-directed neutralizing antibody LP5 Fab in complex with SARS-CoV-2 S2P spike Deposited 2021-05-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.46 Å |
| 7MY2 CryoEM structure of neutralizing nanobody Nb30 in complex with SARS-CoV2 spike Deposited 2021-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5mM Hepes pH7.4, 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 7MY3 CryoEM structure of neutralizing nanobody Nb12 in complex with SARS-CoV2 spike Deposited 2021-05-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；5mM Hepes pH7.4, 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7MY8 Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles Deposited 2021-05-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
816–857（42 aa）
Fragment：residues 816-857
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5；305 K；Ionic strength (raw mmCIF value) 0；Pressure 0
NMR sample composition
0.4 mM [U-99% 15N] Spike Fusion Peptide, Bicelles, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.4 mM [U-99% 13C; U-99% 15N] Spike Fusion Peptide, Bicelles, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 7MZF SARS-CoV-2 receptor binding domain bound to Fab PDI 37 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2 M ammonium sulphate, 20% PEG3350, 0.1 M Tris chloride pH 8.5
|
Resolution 2.49 Å R-free 0.227 |
| 7MZG SARS-CoV-2 receptor binding domain bound to Fab PDI 42 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；10% PEG8000, 0.2 M NaCl, 0.1 M sodium dihydrogen-dipotassium hydrogen phosphate pH 6.2
|
Resolution 2.00 Å R-free 0.236 |
| 7MZH SARS-CoV-2 receptor binding domain bound to Fab WCSL 119 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；14% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.10 Å R-free 0.265 |
| 7MZH SARS-CoV-2 receptor binding domain bound to Fab WCSL 119 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；14% PEG3350, 0.2 M potassium thiocyanate
|
Resolution 2.10 Å R-free 0.265 |
| 7MZI SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | GOL GLYCEROL × 14 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；18% PEG3350, 0.1 M tri sodium citrate pH 5.5
|
Resolution 1.85 Å R-free 0.207 |
| 7MZJ SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 93 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；23% PEG3350, 0.1 M sodium acetate pH 4.5
|
Resolution 2.40 Å R-free 0.268 |
| 7MZJ SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 93 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；23% PEG3350, 0.1 M sodium acetate pH 4.5
|
Resolution 2.40 Å R-free 0.268 |
| 7MZK SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 96 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Tri-sodium citrate pH 5.5, 10% PEG8000
|
Resolution 2.25 Å R-free 0.235 |
| 7MZK SARS-CoV-2 receptor binding domain bound to Fab WCSL 129 and Fab PDI 96 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | CIT CITRIC ACID × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1 M Tri-sodium citrate pH 5.5, 10% PEG8000
|
Resolution 2.25 Å R-free 0.235 |
| 7MZL SARS-CoV-2 receptor binding domain bound to Fab PDI 210 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG6000, 0.1% (w/v) n-Octyl-b-D-glucoside
|
Resolution 3.70 Å R-free 0.256 |
| 7MZM SARS-CoV-2 receptor binding domain bound to Fab PDI 215 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | IPA ISOPROPYL ALCOHOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；in 12% isopropanol, 12% PEG4000, 0.1 M tri sodium citrate pH 5.6
|
Resolution 2.30 Å R-free 0.257 |
| 7MZN SARS-CoV-2 receptor binding domain bound to Fab PDI 231 Deposited 2021-05-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；18% PEG3350, 10% N,N-Dimethyldodecylamine N-oxide (LDAO), 0.2 M sodium sulphate
|
Resolution 3.10 Å R-free 0.259 |
| 7N0G CryoEm structure of SARS-CoV-2 spike protein (S-6P, 1-up) in complex with sybodies (Sb45) Deposited 2021-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 7N0H CryoEM structure of SARS-CoV-2 spike protein (S-6P, 2-up) in complex with sybodies (Sb45) Deposited 2021-05-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 7N1A SARS-CoV-2 YLQ peptide binds to HLA-A2 Deposited 2021-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.2M Potassium thiocyanate (pH 7.0), 22% (w/v) PEG 3350
|
Resolution 2.06 Å R-free 0.241 |
| 7N1A SARS-CoV-2 YLQ peptide binds to HLA-A2 Deposited 2021-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.2M Potassium thiocyanate (pH 7.0), 22% (w/v) PEG 3350
|
Resolution 2.06 Å R-free 0.241 |
| 7N1B SARS-CoV-2 RLQ peptide binds to HLA-A2 Deposited 2021-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1000–1008（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.2M Ammonium sulfate, 0.1M MES (pH 6.5), 20% (w/v) PEG 8000 by micro-seeding
|
Resolution 2.81 Å R-free 0.269 |
| 7N1B SARS-CoV-2 RLQ peptide binds to HLA-A2 Deposited 2021-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
1000–1008（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.2M Ammonium sulfate, 0.1M MES (pH 6.5), 20% (w/v) PEG 8000 by micro-seeding
|
Resolution 2.81 Å R-free 0.269 |
| 7N1E SARS-CoV-2 RLQ peptide-specific TCR pRLQ3 binds to RLQ-HLA-A2 Deposited 2021-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
1000–1008（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；0.2M Ammonium sulfate, 0.1M MES (pH 6.0), 12% (w/v) PEG 4000
|
Resolution 2.30 Å R-free 0.258 |
| 7N1F SARS-CoV-2 YLQ peptide-specific TCR pYLQ7 binds to YLQ-HLA-A2 Deposited 2021-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；in 0.1M Ammonium sulfate, 0.3M Sodium formate, 0.1M Sodium acetate (pH 5.0), 3% (w/v) Gama-PGA (Na+ form, LM), 3% (w/v) PEG 20000
|
Resolution 2.39 Å R-free 0.236 |
| 7N1Q Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants Deposited 2021-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å R-free 0.425 |
| 7N1T Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants Deposited 2021-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å R-free 0.425 |
| 7N1U Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants Deposited 2021-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 7N1V Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants Deposited 2021-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å R-free 0.437 |
| 7N1W Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants Deposited 2021-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 7N1X Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants Deposited 2021-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7N1Y Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants Deposited 2021-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7N3I Crystal structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment C098 Deposited 2021-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–533（206 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298 K；0.05 M citric acid, 0.05M BIS-TRIS propane pH 5.0, 14% PEG 3350
|
Resolution 2.03 Å R-free 0.208 |
| 7N4I Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2057. Deposited 2021-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3,350
|
Resolution 2.28 Å R-free 0.238 |
| 7N4J Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2173. Deposited 2021-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.09M NPS (Sodium nitrate, Sodium phosphate dibasic, Ammonium sulfate), 0.1M buffer system 3 (Tris base and BICINE, pH 8.5), 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350)
|
Resolution 2.21 Å R-free 0.207 |
| 7N4L Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2125. Deposited 2021-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.12 M alcohol mixture (1,6-Hexanediol; 1-Butanol; 1,2-Propanediol; 2-Propanol; 1,4-Butanediol; 1,3-Propanediol), 0.1M buffer system 3 (Tris base and BICINE, pH 8.5), 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) and 0.1 M Manganese(II) chloride tetrahydrate
|
Resolution 3.60 Å R-free 0.329 |
| 7N4M Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibody WRAIR-2151. Deposited 2021-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Ammonium sulfate
|
Resolution 3.79 Å R-free 0.317 |
| 7N5H Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2021-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot time 3s
wait time 30s
blot force 0
|
Resolution 3.24 Å |
| 7N62 SARS-CoV-2 Spike (2P) in complex with C12C9 Fab (NTD local reconstruction) Deposited 2021-06-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7N64 SARS-CoV-2 Spike (2P) in complex with G32R7 Fab (RBD and NTD local reconstruction) Deposited 2021-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7N6D HLA peptide complex Deposited 2021-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；20% PEG3350, 0.2 M sodium thiocyanate
|
Resolution 2.30 Å R-free 0.247 |
| 7N6D HLA peptide complex Deposited 2021-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；20% PEG3350, 0.2 M sodium thiocyanate
|
Resolution 2.30 Å R-free 0.247 |
| 7N6D HLA peptide complex Deposited 2021-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；20% PEG3350, 0.2 M sodium thiocyanate
|
Resolution 2.30 Å R-free 0.247 |
| 7N6D HLA peptide complex Deposited 2021-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain O
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；20% PEG3350, 0.2 M sodium thiocyanate
|
Resolution 2.30 Å R-free 0.247 |
| 7N6E TCR peptide HLA-A2 complex Deposited 2021-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG3350, 0.2 M sodium thiocyanate, 100 mM Tris-Cl
|
Resolution 3.20 Å R-free 0.294 |
| 7N6E TCR peptide HLA-A2 complex Deposited 2021-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain F
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；20% PEG3350, 0.2 M sodium thiocyanate, 100 mM Tris-Cl
|
Resolution 3.20 Å R-free 0.294 |
| 7N8H SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 Global Refinement Deposited 2021-06-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 7N8I SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 (Local Refinement of the NTD/S2L20) Deposited 2021-06-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7N9A Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS RBD with NB21 Deposited 2021-06-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
334–528（195 aa）
Fragment：Receptor Binding Domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7N9B Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS with NB21 Deposited 2021-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7N9C Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS with NB95 Deposited 2021-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.71 Å |
| 7N9E Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting novel and conserved epitopes-CovS with NB34 Deposited 2021-06-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7N9T CryoEM structure of SARS-CoV-2 Spike in complex with Nb17 Deposited 2021-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
25–1147（1123 aa）
Chain B
25–1147（1123 aa）
Chain C
25–1147（1123 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 7NAB Crystal structure of human neutralizing mAb CV3-25 binding to SARS-CoV-2 S MPER peptide 1140-1165 Deposited 2021-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1140–1165（26 aa）
Fragment：SARS-CoV-2 S2 peptide (1140-1165)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；10mg/mL CV3-25 Fab mixed with 10-fold (molar-ratio) of S2 peptide (1140-1165), 0.1M Na citrate pH 5.6, 20% PEG4000, 20% isopropanol
|
Resolution 2.15 Å R-free 0.238 |
| 7NAB Crystal structure of human neutralizing mAb CV3-25 binding to SARS-CoV-2 S MPER peptide 1140-1165 Deposited 2021-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1140–1165（26 aa）
Fragment：SARS-CoV-2 S2 peptide (1140-1165)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NA SODIUM ION × 6 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；10mg/mL CV3-25 Fab mixed with 10-fold (molar-ratio) of S2 peptide (1140-1165), 0.1M Na citrate pH 5.6, 20% PEG4000, 20% isopropanol
|
Resolution 2.15 Å R-free 0.238 |
| 7ND3 EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7ND4 EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-88 Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7ND5 EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7ND6 EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.30 Å |
| 7ND7 EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-316 Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7ND8 EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-384 Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7ND9 EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-253H55L Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7NDA EM structure of SARS-CoV-2 Spike glycoprotein (all RBD down) in complex with COVOX-253H55L Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7NDB EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-253H165L Fab Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 7NDC EM structure of SARS-CoV-2 Spike glycoprotein (all RBD down) in complex with COVOX-159 Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7NDD EM structure of SARS-CoV-2 Spike glycoprotein (one RBD up) in complex with COVOX-159 Deposited 2021-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7NEH Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-269 Fab Deposited 2021-02-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–528（196 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 19 NO3 NITRATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；294 K；0.09 M NPS, 0.1 M sodium HEPES and MOPS, 30% EDO_P8K
|
Resolution 1.77 Å R-free 0.198 |
| 7NKT RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226 Deposited 2021-02-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain AAA
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；50mM K2HPO4, 20% (w/v) PEG 8000
|
Resolution 2.30 Å R-free 0.224 |
| 7NLL SARS-CoV-2 Spike RBD (dimer) in complex with two Fu2 nanobodies Deposited 2021-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
319–540（222 aa）
Chain D
319–540（222 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 7NP1 Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360 Deposited 2021-02-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；16% PEG3350
0.2 M ammonium citrate tribasic
|
Resolution 2.80 Å R-free 0.281 |
| 7NP1 Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360 Deposited 2021-02-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；16% PEG3350
0.2 M ammonium citrate tribasic
|
Resolution 2.80 Å R-free 0.281 |
| 7NP1 Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360 Deposited 2021-02-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；16% PEG3350
0.2 M ammonium citrate tribasic
|
Resolution 2.80 Å R-free 0.281 |
| 7NP1 Crystal Structure of the SARS-CoV-2 Receptor Binding Domain in Complex with Antibody ION-360 Deposited 2021-02-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；16% PEG3350
0.2 M ammonium citrate tribasic
|
Resolution 2.80 Å R-free 0.281 |
| 7NS6 SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies Deposited 2021-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain I
1–1208（1208 aa）
Chain J
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
Chain L
1–1208（1208 aa）
Chain M
1–1208（1208 aa）
Chain N
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 46 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 7NT9 Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (closed conformation) Deposited 2021-03-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | BLA BILIVERDINE IX ALPHA × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；150 mM NaCl, 1 mM ethylenediaminetetraacetic acid (EDTA), 25 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 7NTA Trimeric SARS-CoV-2 spike ectodomain in complex with biliverdin (one RBD erect) Deposited 2021-03-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | BLA BILIVERDINE IX ALPHA × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；150 mM NaCl, 1 mM ethylenediaminetetraacetic acid (EDTA), 25 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7NTC Trimeric SARS-CoV-2 spike ectodomain bound to P008_056 Fab Deposited 2021-03-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | BLA BILIVERDINE IX ALPHA × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；150 mM NaCl, 1 mM ethylenediaminetetraacetic acid (EDTA), 25 mM Tris-HCl, pH 8.0
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7NX6 Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs Deposited 2021-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | CL CHLORIDE ION × 7 SO4 SULFATE ION × 10 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000
|
Resolution 2.25 Å R-free 0.248 |
| 7NX7 Crystal structure of the K417N mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs Deposited 2021-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 13 CL CHLORIDE ION × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000.
|
Resolution 2.30 Å R-free 0.239 |
| 7NX8 Crystal structure of the K417T mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs Deposited 2021-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 4 SO4 SULFATE ION × 12 CIT CITRIC ACID × 1 CL CHLORIDE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000.
|
Resolution 1.95 Å R-free 0.246 |
| 7NX9 Crystal structure of the N501Y mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and EY6A Fabs Deposited 2021-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | SO4 SULFATE ION × 10 GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000.
|
Resolution 2.40 Å R-free 0.229 |
| 7NXA Crystal structure of the receptor binding domain of SARS-CoV-2 B.1.351 variant Spike glycoprotein in complex with COVOX-222 and EY6A Fabs Deposited 2021-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | SO4 SULFATE ION × 19 GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000.
|
Resolution 2.50 Å R-free 0.253 |
| 7NXB Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with COVOX-222 and EY6A Fabs Deposited 2021-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | SO4 SULFATE ION × 15 GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；0.15 M Lithium sulfate, 0.1 M Citric acid pH 3.5, 18% w/v PEG 6,000
|
Resolution 2.67 Å R-free 0.246 |
| 7NXC Crystal structure of the receptor binding domain of SARS-CoV-2 P.1 variant Spike glycoprotein in complex with ACE2 Deposited 2021-03-17 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–528（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；294 K；0.1 M Imidazole pH 7.0 and 20% w/v Polyethylene glycol 6,000
|
Resolution 3.14 Å R-free 0.278 |
| 7OAN Nanobody C5 bound to Spike Deposited 2021-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；Standard buffer
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7OAO Nanobody C5 bound to RBD Deposited 2021-04-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain EEE
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2 M Sodium Acetate, 0.1 M Sodium Cacodylate pH 6.5, 30 % w/v PEG 8000
|
Resolution 1.50 Å R-free 0.186 |
| 7OAP Nanobody H3 AND C1 bound to RBD Deposited 2021-04-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain EEE
331–532（202 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CIT CITRIC ACID × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000
|
Resolution 1.90 Å R-free 0.204 |
| 7OAQ Nanobody H3 AND C1 bound to RBD with Kent mutation Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain EEE
330–532（203 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CIT CITRIC ACID × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.0 M Lithium chloride, 0.1 M Citrate pH 4, 20 % Peg 6000
|
Resolution 1.55 Å R-free 0.178 |
| 7OAU Nanobody C5 bound to Kent variant RBD (N501Y) Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain AAA
330–532（203 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium fluoride and 20 % Peg 3350
|
Resolution 1.65 Å R-free 0.199 |
| 7OAU Nanobody C5 bound to Kent variant RBD (N501Y) Deposited 2021-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain EEE
330–532（203 aa）
|
Mutation：N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium fluoride and 20 % Peg 3350
|
Resolution 1.65 Å R-free 0.199 |
| 7OAY Nanobody F2 bound to RBD Deposited 2021-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain AAA
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M SPG, pH 8, 25 % Peg 1500,
|
Resolution 2.34 Å R-free 0.228 |
| 7OAY Nanobody F2 bound to RBD Deposited 2021-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain CCC
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M SPG, pH 8, 25 % Peg 1500,
|
Resolution 2.34 Å R-free 0.228 |
| 7OAY Nanobody F2 bound to RBD Deposited 2021-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain EEE
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M SPG, pH 8, 25 % Peg 1500,
|
Resolution 2.34 Å R-free 0.228 |
| 7OAY Nanobody F2 bound to RBD Deposited 2021-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain GGG
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M SPG, pH 8, 25 % Peg 1500,
|
Resolution 2.34 Å R-free 0.228 |
| 7OAY Nanobody F2 bound to RBD Deposited 2021-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain III
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M SPG, pH 8, 25 % Peg 1500,
|
Resolution 2.34 Å R-free 0.228 |
| 7OAY Nanobody F2 bound to RBD Deposited 2021-04-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain KKK
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M SPG, pH 8, 25 % Peg 1500,
|
Resolution 2.34 Å R-free 0.228 |
| 7OD3 SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C3 symmetry Deposited 2021-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | EIC LINOLEIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.80 Å |
| 7ODL SARS CoV-2 Spike protein, Bristol UK Deletion variant, Closed conformation, C1 symmetry Deposited 2021-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | EIC LINOLEIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.03 Å |
| 7OLZ Crystal structure of the SARS-CoV-2 RBD with neutralizing-VHHs Re5D06 and Re9F06 Deposited 2021-05-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
|
Not recorded | DMX 3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M MOPS pH 7.5, 2.07 M ammonium sulfate, 0.1 M NDSB-256
|
Resolution 1.75 Å R-free 0.209 |
| 7OR9 Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-222 and COVOX-278 Fabs Deposited 2021-06-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 2 CL CHLORIDE ION × 4 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M amino acids (Glu, Ala, Gly, Lys, Ser), 0.1 M MES/imidazole pH 6.5, 10% (w/v) PEG 20000 and 20% (v/v) PEG MME 550.
|
Resolution 2.34 Å R-free 0.230 |
| 7ORA Crystal structure of the T478K mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-45 and COVOX-253 Fabs Deposited 2021-06-04 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
333–528（196 aa）
|
Mutation：T478K | GOL GLYCEROL × 3 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BICINE pH 8.5 and 20% (w/v) PEG 10,000
|
Resolution 2.60 Å R-free 0.245 |
| 7ORA Crystal structure of the T478K mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-45 and COVOX-253 Fabs Deposited 2021-06-04 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
333–528（196 aa）
|
Mutation：T478K | GOL GLYCEROL × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BICINE pH 8.5 and 20% (w/v) PEG 10,000
|
Resolution 2.60 Å R-free 0.245 |
| 7ORB Crystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 Fabs Deposited 2021-06-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 9 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-TRIS pH 6.5 and 16% (w/v) PEG 10000
|
Resolution 2.50 Å R-free 0.251 |
| 7ORB Crystal structure of the L452R mutant receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with COVOX-75 and COVOX-253 Fabs Deposited 2021-06-04 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain X
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 7 PEG DI(HYDROXYETHYL)ETHER × 3 CL CHLORIDE ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PO4 PHOSPHATE ION × 2 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-TRIS pH 6.5 and 16% (w/v) PEG 10000
|
Resolution 2.50 Å R-free 0.251 |
| 7OWX Structure of coiled-coil tetramer from SARS-CoV-2 spike stalk region Deposited 2021-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric |
Chain A
1177–1203（27 aa）
Chain B
1177–1203（27 aa）
Chain C
1177–1203（27 aa）
Chain D
1177–1203（27 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.002 M zinc chloride, 0.1 M Tris pH 8, 20 % w/v PEG 6000
|
Resolution 1.93 Å R-free 0.233 |
| 7P19 Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2 Deposited 2021-07-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
334–541（208 aa）
|
Mutation：Q498Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M sodium phosphate pH 6.5, 12% w/v PEG 8000
|
Resolution 3.24 Å R-free 0.288 |
| 7P19 Crystal structure of SARS-CoV-2 RBD Q498Y complexed with human ACE2 Deposited 2021-07-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
334–541（208 aa）
|
Mutation：Q498Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M sodium phosphate pH 6.5, 12% w/v PEG 8000
|
Resolution 3.24 Å R-free 0.288 |
| 7P3D MHC I A02 Allele presenting YLQPRTFLL Deposited 2021-07-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
269–277（9 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 ACT ACETATE ION × 1 CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium nitrate, 0.1 M Bis Tris propane pH 7.5, and 20 % w/v PEG 3350
|
Resolution 1.67 Å R-free 0.231 |
| 7P5G NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506 fragment in HFIP/H2O Deposited 2021-07-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
482–506（25 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 2.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
2.5 mM SMIMIC-OR, 50 % v/v Hexafluoroisopropanol, 40 % v/v H2O, 10 % v/v [U-100% 2H] D2O, 50% hexafluoroisopropanol/40% H2O/10% D2O | 50% hexafluoroisopropanol/40% H2O/10% D2O
|
Resolution not provided |
| 7P5Q NMR structure of a peptide deriving from SARS-CoV-2 Lineage B.1.1.7 S RBD 482-506 fragment in HFIP/H2O Deposited 2021-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
482–506（25 aa）
|
Mutation：N501Y | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 2.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
2.5 mM SMIMIC-a, 50 % v/v Hexafluoroisopropanol, 40 % v/v H2O, 10 % v/v [U-100% 2H] D2O, 50% hexafluoroisopropanol/40% H2O/10% D2O | 50% hexafluoroisopropanol/40% H2O/10% D2O
|
Resolution not provided |
| 7P5S NMR structure of a peptide deriving from SARS-CoV-2 Lineages P.1 and B.1.351 S RBD 482-506 fragment in HFIP/H2O Deposited 2021-07-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
482–506（25 aa）
|
Mutation：E484K, N501Y | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 2.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure 1
NMR sample composition
2.5 mM SMIMIC-bg, 50 % v/v Hexafluoroisopropanol, 40 % v/v H2O, 10 % v/v [U-100% 2H] D2O, 50% hexafluoroisopropanol/40% H2O/10% D2O | 50% hexafluoroisopropanol/40% H2O/10% D2O
|
Resolution not provided |
| 7P77 SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 3up conformation Deposited 2021-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris-HCl pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.98 Å |
| 7P78 SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 1up/1up-out/1down conformation Deposited 2021-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris-HCl pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.32 Å |
| 7P79 SARS-CoV-2 spike protein in complex with sybodyb#15 in a 1up/1up-out/1down conformation. Deposited 2021-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris-HCl pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.00 Å |
| 7P7A SARS-CoV-2 spike protein in complex with sybody#68 in a 2up/1flexible conformation Deposited 2021-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris-HCl pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 4.76 Å |
| 7P7B SARS-CoV-2 spike protein in complex with sybody no68 in a 1up/2down conformation Deposited 2021-07-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris-HCl pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.13 Å |
| 7PBE Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope Deposited 2021-08-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
269–277（9 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M ammonium sulphate, 0.1 M Tris, pH 8.5, and 25 % w/v PEG 4000
|
Resolution 3.00 Å R-free 0.296 |
| 7PBE Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope Deposited 2021-08-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain H
269–277（9 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M ammonium sulphate, 0.1 M Tris, pH 8.5, and 25 % w/v PEG 4000
|
Resolution 3.00 Å R-free 0.296 |
| 7PQY Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A Fab Deposited 2021-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.08 M sodium citrate tribasic and 24% (w/v) PEG 550.
|
Resolution 3.00 Å R-free 0.245 |
| 7PQY Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A Fab Deposited 2021-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.08 M sodium citrate tribasic and 24% (w/v) PEG 550.
|
Resolution 3.00 Å R-free 0.245 |
| 7PQZ Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FI-3A and FD-11A Fabs Deposited 2021-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | PO4 PHOSPHATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.9 M sodium formate pH 7.0
|
Resolution 3.20 Å R-free 0.240 |
| 7PR0 Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab Deposited 2021-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 3 NO3 NITRATE ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% (w/v) PEG 20 000, 20% (v/v) PEG MME 550, 0.03 M of each NPS (NaNO3; Na2HPO4; (NH4)2SO4) and 0.1 M bicine/Trizma base pH 8.5.
|
Resolution 2.92 Å R-free 0.251 |
| 7PR0 Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab Deposited 2021-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NO3 NITRATE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% (w/v) PEG 20 000, 20% (v/v) PEG MME 550, 0.03 M of each NPS (NaNO3; Na2HPO4; (NH4)2SO4) and 0.1 M bicine/Trizma base pH 8.5.
|
Resolution 2.92 Å R-free 0.251 |
| 7PR0 Crystal structure of the receptor binding domain of SARS-CoV-2 Spike glycoprotein in complex with FD-5D Fab Deposited 2021-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% (w/v) PEG 20 000, 20% (v/v) PEG MME 550, 0.03 M of each NPS (NaNO3; Na2HPO4; (NH4)2SO4) and 0.1 M bicine/Trizma base pH 8.5.
|
Resolution 2.92 Å R-free 0.251 |
| 7PRY Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with COVOX-45 and beta-6 Fabs Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain I
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, and 18% (w/v) PEG 20000
|
Resolution 3.10 Å R-free 0.291 |
| 7PRY Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with COVOX-45 and beta-6 Fabs Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, and 18% (w/v) PEG 20000
|
Resolution 3.10 Å R-free 0.291 |
| 7PRZ Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-22 Fabs Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | SO4 SULFATE ION × 15 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；containing 0.2 M Lithium sulfate, 0.1 M MES pH 6.0 and 20% (w/v) PEG 4000
|
Resolution 3.20 Å R-free 0.223 |
| 7PS0 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-24 Fabs Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M Tris pH 7.5 and 20% (w/v) PEG 5000 MME.
|
Resolution 2.92 Å R-free 0.271 |
| 7PS0 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with beta-24 Fabs Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M Tris pH 7.5 and 20% (w/v) PEG 5000 MME.
|
Resolution 2.92 Å R-free 0.271 |
| 7PS1 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-27 Fab Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 4 CL CHLORIDE ION × 4 IOD IODIDE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Potassium iodide, 0.1 M MES pH 6.5 and 25% (w/v) PEG 4000.
|
Resolution 2.40 Å R-free 0.215 |
| 7PS2 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-29 and Beta-53 Fabs Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 2 SO4 SULFATE ION × 14 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5 and 1.5 M Ammonium sulfate.
|
Resolution 2.99 Å R-free 0.266 |
| 7PS4 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-38 Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.8 M Sodium/potassium phosphate pH 7.5
|
Resolution 1.94 Å R-free 0.231 |
| 7PS4 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-38 Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.8 M Sodium/potassium phosphate pH 7.5
|
Resolution 1.94 Å R-free 0.231 |
| 7PS5 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-47 Fab Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Potassium chloride, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 2000 MME
|
Resolution 3.14 Å R-free 0.274 |
| 7PS6 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-44 and Beta-54 Fabs Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 GOL GLYCEROL × 2 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Citric acid pH 3.5 and 25% (w/v) PEG 3350
|
Resolution 2.26 Å R-free 0.240 |
| 7PS7 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-40 Fab Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.02 M of each carboxylic acid and 0.1 M MES/imidazole pH 6.5
|
Resolution 3.90 Å R-free 0.284 |
| 7PS7 Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-40 Fab Deposited 2021-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.02 M of each carboxylic acid and 0.1 M MES/imidazole pH 6.5
|
Resolution 3.90 Å R-free 0.284 |
| 7Q0A SARS-CoV-2 Spike ectodomain with Fab FI3A Deposited 2021-10-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 7Q0G Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-49 and FI-3A Fabs Deposited 2021-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 13 CL CHLORIDE ION × 14 K POTASSIUM ION × 14 TAR D(-)-TARTARIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M BIS-TRIS pH 6.5, 10% w/v Polyethylene glycol 10,000
|
Resolution 1.82 Å R-free 0.224 |
| 7Q0H Crystal structure of the receptor binding domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-50 and Beta-54 Deposited 2021-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.0, 28% w/v Polyethylene glycol 4,000
|
Resolution 3.65 Å R-free 0.303 |
| 7Q0I Crystal structure of the N-terminal domain of SARS-CoV-2 beta variant spike glycoprotein in complex with Beta-43 Deposited 2021-10-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
13–305（293 aa）
Chain D
13–305（293 aa）
|
Not recorded | CL CHLORIDE ION × 6 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 3 PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES, 25 % w/v PEG 2000 MME
|
Resolution 2.39 Å R-free 0.242 |
| 7Q1Z Structure of formaldehyde cross-linked SARS-CoV-2 S glycoprotein Deposited 2021-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7Q6E Beta049 fab in complex with SARS-CoV2 beta-Spike glycoprotein, The Beta mAb response underscores the antigenic distance to other SARS-CoV-2 variants Deposited 2021-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1205（1205 aa）
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7Q9F Beta-50 fab in complex with SARS-CoV-2 beta-Spike glycoprotein Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7Q9G COVOX-222 fab in complex with SARS-CoV-2 beta-Spike glycoprotein Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7Q9I Beta-43 fab in complex with SARS-CoV-2 beta-Spike glycoprotein Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 7Q9J Beta-26 fab in complex with SARS-CoV-2 beta-Spike glycoprotein Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1205（1205 aa）
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7Q9K Beta-32 fab in complex with SARS-CoV-2 beta-Spike glycoprotein Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7Q9M Beta-53 fab in complex with SARS-CoV-2 beta-Spike glycoprotein Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7Q9P Beta-06 fab in complex with SARS-CoV-2 beta-Spike glycoprotein Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1205（1205 aa）
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7QDG SARS-CoV-2 S protein S:A222V + S:D614G mutant 1-up Deposited 2021-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–1213（1199 aa）
Chain B
15–1213（1199 aa）
Chain C
15–1213（1199 aa）
|
Mutation：S:A222V + S:D614G Mutation：S:A222V + S:D614G Mutation：S:A222V + S:D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7QDH SARS-CoV-2 S protein S:D614G mutant 1-up Deposited 2021-11-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–1213（1199 aa）
Chain B
15–1213（1199 aa）
Chain C
15–1213（1199 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7QEZ Crystal structure of the SARS-CoV-2 RBD in complex with the ultrapotent antibody CV2.1169 and CR3022 Deposited 2021-12-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
331–528（198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；15% PEG 8000, 0.5 M lithium sulfate
|
Resolution 2.89 Å R-free 0.281 |
| 7QF0 Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.2325 Deposited 2021-12-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–528（198 aa）
|
Not recorded | NA SODIUM ION × 1 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；296 K；0.1 M ammonium citrate (pH 7.0), 12% PEG 3350,
|
Resolution 2.30 Å R-free 0.221 |
| 7QF1 Crystal structure of the SARS-CoV-2 RBD in complex with the human antibody CV2.6264 Deposited 2021-12-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
331–528（198 aa）
Chain F
331–528（198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；296 K；0.1 M NaAc, 7% PEG 6000, 30% ethanol
|
Resolution 2.80 Å R-free 0.254 |
| 7QO9 SARS-CoV-2 S Omicron Spike B.1.1.529 - RBD and NTD (Local) Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.88 Å |
| 7QTI SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global) Deposited 2022-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1205（1205 aa）
Chain D
1–1205（1205 aa）
Chain K
1–1205（1205 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 7QUR SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 GE9 2,3,5-tris(iodanyl)benzamide × 3 SIA N-acetyl-alpha-neuraminic acid × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.27 Å |
| 7QUS SARS-CoV-2 Spike, C3 symmetry Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.39 Å |
| 7R0Z Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement) Deposited 2022-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7R10 Dissociated S1 domain of Alpha Variant SARS-CoV-2 Spike bound to ACE2 Deposited 2022-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7R11 Dissociated S1 domain of Beta Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement) Deposited 2022-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7R12 Dissociated S1 domain of Mink Variant SARS-CoV-2 Spike bound to ACE2 (Non-Uniform Refinement) Deposited 2022-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7R13 Alpha Variant SARS-CoV-2 Spike in Closed conformation Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7R14 Alpha Variant SARS-CoV-2 Spike with 1 Erect RBD Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7R16 Beta Variant SARS-CoV-2 Spike with 1 Erect RBD Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7R17 Beta Variant SARS-CoV-2 Spike with 2 Erect RBDs Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7R18 Mink Variant SARS-CoV-2 Spike in Closed conformation Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1146（1146 aa）
Chain B
1–1146（1146 aa）
Chain C
1–1146（1146 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7R19 Mink Variant SARS-CoV-2 Spike with 2 Erect RBDs Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7R1A Furin Cleaved Alpha Variant SARS-CoV-2 Spike in complex with 3 ACE2 Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7R1B Mink Variant SARS-CoV-2 Spike with 1 Erect RBD Deposited 2022-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7R40 Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment Deposited 2022-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7R4I The SARS-CoV-2 spike in complex with the 2.15 neutralizing nanobody Deposited 2022-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7R4Q The SARS-CoV-2 spike in complex with the 1.29 neutralizing nanobody Deposited 2022-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7R4R The SARS-CoV-2 spike in complex with the 1.10 neutralizing nanobody Deposited 2022-02-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7R6W SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2X35 Fab and S309 Fab Deposited 2021-06-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
328–531（204 aa）
Fragment：receptor-binding domain (UNP reisdues 328-531)
|
Not recorded | SO4 SULFATE ION × 23 GOL GLYCEROL × 3 CL CHLORIDE ION × 3 POL N-PROPANOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；1.85 M ammonium sulfate, 0.1 M Tris, pH 8.17, 0.8% w/v polyvinyl alcohol, 1% v/v 1-propanol, 0.01 M HEPES, pH 7
|
Resolution 1.83 Å R-free 0.232 |
| 7R6X SARS-CoV-2 spike receptor-binding domain (RBD) in complex with S2E12 Fab, S309 Fab, and S304 Fab Deposited 2021-06-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain R
328–531（204 aa）
Fragment：receptor-binding domain (UNP residues 328-531)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；Crystal 1: 0.09 M phosphate/citrate, pH 5.5, 27% v/v PEG Smear Low, 4% v/v polypropylene glycol 400, 0.02 M imidazole, pH 7, Crystal 2: 0.09 M phosphate/citrate, pH 5.5, 27% v/v PEG Smear Low, 0.01 M potassium/sodium phosphate, pH 7, 1% v/v PPGBA 230, 1.5% v/v PPGBA 400
|
Resolution 2.95 Å R-free 0.262 |
| 7R7N SARS-CoV-2 spike in complex with the S2D106 neutralizing antibody Fab fragment (local refinement of the RBD and S2D106) Deposited 2021-06-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 7R8L Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody C099 and CR3022 Deposited 2021-06-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
334–528（195 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.1M Sodium cacodylate, 40% 2-Methyl-2,4-pentanediol (MPD), and 5% PEG8000
|
Resolution 2.60 Å R-free 0.229 |
| 7R8M Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C032 Deposited 2021-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.40 Å |
| 7R8N Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C051 Deposited 2021-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain E
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.55 Å |
| 7R8O Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C548 Deposited 2021-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain E
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3s blot, 0 blot force
|
Resolution 3.50 Å |
| 7R95 Membrane bound structure of HR1 domain of SARS-CoV-2 spike protein Deposited 2021-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
919–965（47 aa）
Fragment：Heptad repeat 1 domain, residues 919-965
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR measurement conditions
pH 6；308 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR measurement conditions
pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition
0.4 mM [U-13C; U-15N; U-2H] SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 150 mM DMPC/DHPC, 97% H2O/3% D2O | 97% H2O/3% D2O
NMR sample composition
0.3 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 150 mM DMPC/DHPC, 97% H2O/3% D2O | 97% H2O/3% D2O
NMR sample composition
0.1 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 100 mM DMPC/DHPC, 97% H2O/3% D2O | 97% H2O/3% D2O
NMR sample composition
0.15 mM 15N, 2H SARS-CoV-2 spike protein HR1 domain, 20 mM sodium phosphate buffer, 30 mM NaCl, 120 mM DMPC/DHPC, 97% H2O/3% D2O | 97% H2O/3% D2O
|
Resolution not provided |
| 7RA8 SARS-CoV-2 S glycoprotein in complex with S2X259 Fab Deposited 2021-06-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7RAL SARS-CoV-2 S bound to S2X259 Fab (local refinement of the RBD/S2X259 variable domains) Deposited 2021-07-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7RAQ Crystal structure of CV3-25 Fab bound to SARS-CoV-2 spike stem helix peptide Deposited 2021-07-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain P
1149–1167（19 aa）
|
Not recorded | GOL GLYCEROL × 7 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Na Acetate:HCl, pH 4.5, 2.0M (NH4)2SO4, 0.01M SrCl
|
Resolution 1.74 Å R-free 0.203 |
| 7RBU SARS-CoV-2 Spike in complex with PVI.V6-14 Fab Deposited 2021-07-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
14–307（294 aa）
Fragment：N-terminal domain (UNP residues 14-307)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7RBV SARS-CoV-2 Spike in complex with PVI.V6-14 Fab Deposited 2021-07-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7RBY Crystal structure of Nanobody nb112 and SARS-CoV-2 RBD Deposited 2021-07-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
329–538（210 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Mg(OAc)2, 0.1 M MOPS pH 7.5, 12% w/v PEG8000
|
Resolution 2.82 Å R-free 0.287 |
| 7RBY Crystal structure of Nanobody nb112 and SARS-CoV-2 RBD Deposited 2021-07-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
329–538（210 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1M Mg(OAc)2, 0.1 M MOPS pH 7.5, 12% w/v PEG8000
|
Resolution 2.82 Å R-free 0.287 |
| 7RKU Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022 Deposited 2021-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–533（206 aa）
Fragment：Receptor Binding Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.05M ammonium sulfate, 0.05M BIS-Tris, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)
|
Resolution 3.20 Å R-free 0.231 |
| 7RKU Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022 Deposited 2021-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
328–533（206 aa）
Fragment：Receptor Binding Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.05M ammonium sulfate, 0.05M BIS-Tris, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)
|
Resolution 3.20 Å R-free 0.231 |
| 7RKU Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022 Deposited 2021-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–533（206 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.05M ammonium sulfate, 0.05M BIS-Tris, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)
|
Resolution 3.20 Å R-free 0.231 |
| 7RKU Structure of the SARS-CoV-2 receptor binding domain in complex with the human neutralizing antibody Fab fragment, C022 Deposited 2021-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
328–533（206 aa）
Fragment：Receptor Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.05M ammonium sulfate, 0.05M BIS-Tris, 30% v/v pentaerythritol ethoxylate (15/4 EO/OH)
|
Resolution 3.20 Å R-free 0.231 |
| 7RKV Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C118 (State 1) Deposited 2021-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 7RNJ S2P6 Fab fragment bound to the SARS-CoV/SARS-CoV-2 spike stem helix peptide Deposited 2021-07-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1146–1159（14 aa）
|
Not recorded | SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium sulfate, 0.1 M Sodium acetate pH 4.6, 25% (v/v) PEG Smear Broad
|
Resolution 2.67 Å R-free 0.274 |
| 7RPV Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD Deposited 2021-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
320–537（218 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.2 M ammonium sulfate, 0.1 M MES pH6.5, 20% PEG8000
|
Resolution 3.54 Å R-free 0.292 |
| 7RPV Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD Deposited 2021-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
320–537（218 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.2 M ammonium sulfate, 0.1 M MES pH6.5, 20% PEG8000
|
Resolution 3.54 Å R-free 0.292 |
| 7RPV Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD Deposited 2021-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
320–537（218 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.2 M ammonium sulfate, 0.1 M MES pH6.5, 20% PEG8000
|
Resolution 3.54 Å R-free 0.292 |
| 7RPV Crystal structure of affinity-enhancing and catalytically inactive ACE2 in complex with SARS-CoV-2 RBD Deposited 2021-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
320–537（218 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.2 M ammonium sulfate, 0.1 M MES pH6.5, 20% PEG8000
|
Resolution 3.54 Å R-free 0.292 |
| 7RQ6 Cryo-EM structure of SARS-CoV-2 spike in complex with non-neutralizing NTD-directed CV3-13 Fab isolated from convalescent individual Deposited 2021-08-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.18 Å |
| 7RR0 SARS-CoV-2 receptor binding domain bound to Fab PDI 222 Deposited 2021-08-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 7RTD SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01 Deposited 2021-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2M NaFluoride
|
Resolution 2.05 Å R-free 0.235 |
| 7RTR YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01 Deposited 2021-08-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
269–277（9 aa）
Fragment：epitope YLQPRTFLL (UNP residues 269-277)
|
Not recorded | NA SODIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.05 M Zinc Acetate
|
Resolution 2.60 Å R-free 0.235 |
| 7RU1 SARS-CoV-2-6P-Mut7 S protein (C3 symmetry) Deposited 2021-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 2.80 Å |
| 7RU2 SARS-CoV-2-6P-Mut7 S protein (asymmetric) Deposited 2021-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.00 Å |
| 7RU3 CC6.33 IgG in complex with SARS-CoV-2-6P-Mut7 S protein (non-uniform refinement) Deposited 2021-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.30 Å |
| 7RU4 CC6.33 IgG in complex with SARS-CoV-2-6P-Mut7 S protein (RBD/Fv local refinement) Deposited 2021-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.30 Å |
| 7RU5 CC6.30 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (non-uniform refinement) Deposited 2021-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.60 Å |
| 7RU8 CC6.30 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (RBD/Fv local refinement) Deposited 2021-08-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.80 Å |
| 7RW2 Cryo-EM structure of NTD-directed neutralizing antibody 5-7 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2021-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7RXD CryoEM structure of RBD domain of COVID-19 in complex with Legobody Deposited 2021-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
334–526（193 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7RZQ Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1162–1201（40 aa）
Chain E
1162–1201（40 aa）
Chain F
1162–1201（40 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.09 Å |
| 7RZR Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with D936Y mutation Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1162–1201（40 aa）
Chain E
1162–1201（40 aa）
Chain F
1162–1201（40 aa）
|
Mutation：D936Y Mutation：D936Y Mutation：D936Y | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.27 Å |
| 7RZS Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with L938F mutation Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1162–1201（40 aa）
Chain E
1162–1201（40 aa）
Chain F
1162–1201（40 aa）
|
Mutation：L938F Mutation：L938F Mutation：L938F | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.52 Å |
| 7RZT Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with S940F mutation Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1162–1201（40 aa）
Chain E
1162–1201（40 aa）
Chain F
1162–1201（40 aa）
|
Mutation：S940F Mutation：S940F Mutation：S940F | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.35 Å |
| 7RZU Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with A942S mutation Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1162–1201（40 aa）
Chain E
1162–1201（40 aa）
Chain F
1162–1201（40 aa）
|
Mutation：A942S Mutation：A942S Mutation：A942S | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 7RZV Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with V1176F mutation Deposited 2021-08-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1157–1201（45 aa）
Chain E
1157–1201（45 aa）
Chain F
1157–1201（45 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.11 Å |
| 7S0B Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody N-612-056 Deposited 2021-08-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
319–533（215 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M Lithium citrate tribasic tetrahydrate and 20% w/v polyethylene glycol 3,350
|
Resolution 2.90 Å R-free 0.260 |
| 7S0B Structure of the SARS-CoV-2 RBD in complex with neutralizing antibody N-612-056 Deposited 2021-08-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–533（215 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M Lithium citrate tribasic tetrahydrate and 20% w/v polyethylene glycol 3,350
|
Resolution 2.90 Å R-free 0.260 |
| 7S0C Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody N-612-017 Deposited 2021-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 7S0D Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody N-612-014 Deposited 2021-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7S0E Structure of the SARS-CoV-2 S1 subunit in complex with antibody N-612-004 Deposited 2021-08-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 7S3N SARS-CoV-2 S stem helix peptide bound to Fab22 Deposited 2021-09-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1146–1164（19 aa）
Fragment：stem helix peptide (UNP residues 1146-1164)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate, pH 5.5, 23% PEG8000
|
Resolution 1.90 Å R-free 0.235 |
| 7S4S Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex CoV11 Fab Deposited 2021-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 5 ACT ACETATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；15% PEG 4000
150 mM ammonium sulfate
0.1 M MES pH 6.0
|
Resolution 2.05 Å R-free 0.198 |
| 7S5P Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibody CS23 Deposited 2021-09-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 13 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；293.15 K；1.6 M ammonium sulfate and 0.1 M bicine pH 9.0
|
Resolution 2.86 Å R-free 0.247 |
| 7S5Q Crystal structure of SARS-CoV-2 B.1.351 variant receptor binding domain in complex with neutralizing antibodies CS44 and COVA1-16 Deposited 2021-09-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；1.6 M ammonium sulfate and 0.1 M citric acid pH 4.0
|
Resolution 2.88 Å R-free 0.257 |
| 7S5R Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibodies CV07-287 and COVA1-16 Deposited 2021-09-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；293.15 K；1.6 M ammonium sulfate and 0.1 M bicine pH 9.0
|
Resolution 2.45 Å R-free 0.237 |
| 7S6I SARS-CoV-2-6P-Mut2 S protein Deposited 2021-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.20 Å |
| 7S6J J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 1) Deposited 2021-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.40 Å |
| 7S6K J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut2 S protein (conformation 2) Deposited 2021-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P Mutation：S383C, R682G, R683S, R685S, F817P, A892P, A899P, A942P, D985C, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 3.40 Å |
| 7S6L J08 fragment antigen binding in complex with SARS-CoV-2-6P-Mut7 S protein (conformation 3) Deposited 2021-09-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；Detergent added shortly before freezing
cryo-EM vitrification conditions
Cryogen ETHANE；3 s blot time
|
Resolution 4.00 Å |
| 7S83 Crystal structure of SARS CoV-2 Spike Receptor Binding Domain in complex with shark neutralizing VNARs ShAb01 and ShAb02 Deposited 2021-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14.5% PEG20000,
0.1M HEPES pH7.0
|
Resolution 2.52 Å R-free 0.278 |
| 7SA2 SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01 Deposited 2021-09-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1060–1068（9 aa）
Fragment：UNP residues 1060-1068
|
Not recorded | CD CADMIUM ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2 M K formate, 1 mM CdCl2
|
Resolution 1.85 Å R-free 0.196 |
| 7SBK Closed state of pre-fusion SARS-CoV-2 Delta variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å R-free 0.425 |
| 7SBL One RBD-up 1 of pre-fusion SARS-CoV-2 Delta variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å R-free 0.425 |
| 7SBO One RBD-up 2 of pre-fusion SARS-CoV-2 Delta variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å R-free 0.425 |
| 7SBP Closed state of pre-fusion SARS-CoV-2 Kappa variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å R-free 0.425 |
| 7SBQ One RBD-up 1 of pre-fusion SARS-CoV-2 Kappa variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å R-free 0.437 |
| 7SBR One RBD-up 2 of pre-fusion SARS-CoV-2 Kappa variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å R-free 0.437 |
| 7SBS One RBD-up 1 of pre-fusion SARS-CoV-2 Gamma variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å R-free 0.437 |
| 7SBT One RBD-up 2 of pre-fusion SARS-CoV-2 Gamma variant spike protein Deposited 2021-09-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å R-free 0.437 |
| 7SBU Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a highly potent antibody J08 Fab Deposited 2021-09-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；17% (w/v) PEG 4000, 15% (v/v) Glycerol, 8.5% (v/v) Isopropanol, 0.085 M Sodium HEPES pH 7.5
|
Resolution 2.53 Å R-free 0.261 |
| 7SC1 Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, R40-1G8 Deposited 2021-09-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7SD5 Crystallographic structure of neutralizing antibody 10-40 in complex with SARS-CoV-2 spike receptor binding domain Deposited 2021-09-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
Fragment：receptor binding domain (UNP residues 319-537)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；310 K；0.2 M potassium thiocyanate, 0.1 M sodium acetate, pH 5.5, 8% PEG550 MME, 8% PEG20000
|
Resolution 1.53 Å R-free 0.206 |
| 7SI2 Crystal structure of neutralizing antibody 10-28 in complex with SARS-CoV-2 spike receptor binding domain (RBD) Deposited 2021-10-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–537（219 aa）
Fragment：receptor-binding domain (UNP reisdues 319-537)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350, 30% PEG2000 MME
|
Resolution 3.20 Å R-free 0.261 |
| 7SI2 Crystal structure of neutralizing antibody 10-28 in complex with SARS-CoV-2 spike receptor binding domain (RBD) Deposited 2021-10-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–537（219 aa）
Fragment：receptor-binding domain (UNP reisdues 319-537)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350, 30% PEG2000 MME
|
Resolution 3.20 Å R-free 0.261 |
| 7SI2 Crystal structure of neutralizing antibody 10-28 in complex with SARS-CoV-2 spike receptor binding domain (RBD) Deposited 2021-10-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
Fragment：receptor-binding domain (UNP reisdues 319-537)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG3350, 30% PEG2000 MME
|
Resolution 3.20 Å R-free 0.261 |
| 7SIS SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01 Deposited 2021-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
976–984（9 aa）
Fragment：UNP residues 976-984
|
Not recorded | ACT ACETATE ION × 1 CD CADMIUM ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；20% PEG 3350, 0.2M Ammonium Formate, 1 mM CdCl2
|
Resolution 1.90 Å R-free 0.206 |
| 7SJ0 Antibody A7V3 bound to N-terminal domain of the spike Deposited 2021-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris pH 7.5, 200 mM NaCl, 0.02% NaN3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 7SJS Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CC40.8 Deposited 2021-10-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1140–1164（25 aa）
|
Not recorded | ACT ACETATE ION × 1 SO4 SULFATE ION × 5 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.26；293.15 K；0.1 M sodium acetate buffer at pH 4.26, 0.2 M ammonium sulfate, and 28% (w/v) polyethylene glycol monomethyl ether 2000
|
Resolution 1.61 Å R-free 0.206 |
| 7SN2 Structure of human SARS-CoV-2 neutralizing antibody C1C-A3 Fab Deposited 2021-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 4-6 seconds
|
Resolution 4.30 Å |
| 7SN3 Structure of human SARS-CoV-2 spike glycoprotein trimer bound by neutralizing antibody C1C-A3 Fab (variable region) Deposited 2021-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 4-6 seconds
|
Resolution 3.10 Å |
| 7SO9 SARS-CoV-2 S B.1.617.2 delta variant + S2M11 + S2L20 Global Refinement Deposited 2021-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 7SOA SARS-CoV-2 S NTD B.1.617.2 delta variant + S2L20 Local Refinement Deposited 2021-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7SOB SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement Deposited 2021-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 7SOC SARS-CoV-2 S RBD B.1.617.1 kappa variant S309 Local Refinement Deposited 2021-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7SOD SARS-CoV-2 S NTD B.1.617.1 kappa variant S2L20 Local Refinement Deposited 2021-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7SOE SARS-CoV-2 S B.1.617.1 kappa variant + S2X303 Global Refinement Deposited 2021-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7SOF SARS-CoV-2 S NTD B.1.617.1 kappa variant S2X303 Local Refinement Deposited 2021-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7SPO Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 3B4 Deposited 2021-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
330–532（203 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium acetate trihydrate, 20 % w/v PEG 3350
|
Resolution 1.92 Å R-free 0.226 |
| 7SPO Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 3B4 Deposited 2021-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–532（203 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Sodium acetate trihydrate, 20 % w/v PEG 3350
|
Resolution 1.92 Å R-free 0.226 |
| 7SPP Crystal structure of the SARS-CoV-2 receptor binding domain in complex with VNAR 2C02 Deposited 2021-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–535（217 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium sulfate and 20 % (w/v) PEG 3350
|
Resolution 1.96 Å R-free 0.224 |
| 7SWN G32A4 Fab in complex with SARS-CoV-2 Spike 6P (RBD local reconstruction) Deposited 2021-11-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
Fragment：RBD domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7SWO C98C7 Fab in complex with SARS-CoV-2 Spike 6P (RBD local reconstruction) Deposited 2021-11-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–528（195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7SWP G32Q4 Fab in complex with SARS-CoV-2 Spike 6P (RBD local reconstruction) Deposited 2021-11-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–528（195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7SWW SARS-CoV-2 Spike NTD in complex with neutralizing Fab SARS2-57 (local refinement) Deposited 2021-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–304（291 aa）
Fragment：N-terminal domain (UNP residues 14-304)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.13 Å |
| 7SWX SARS-CoV-2 Spike in complex with neutralizing Fab SARS2-57 (three down conformation) Deposited 2021-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1146（1133 aa）
Chain B
14–1146（1133 aa）
Chain C
14–1146（1133 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.13 Å |
| 7SXR Cryo-EM structure of the SARS-CoV-2 D614G mutant spike protein ectodomain Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7SXS Cryo-EM structure of the SARS-CoV-2 D614G,L452R mutant spike protein ectodomain Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, L452R Mutation：D614G, L452R Mutation：D614G, L452R | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 7SXT Cryo-EM structure of the SARS-CoV-2 D614G,N501Y mutant spike protein ectodomain Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, N501Y Mutation：D614G, N501Y Mutation：D614G, N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.31 Å |
| 7SXU Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, N501Y, E484K Mutation：D614G, N501Y, E484K Mutation：D614G, N501Y, E484K | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7SXV Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, N501Y, E484K, K417N Mutation：D614G, N501Y, E484K, K417N Mutation：D614G, N501Y, E484K, K417N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 7SXW Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417T mutant spike protein ectodomain Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, N501Y, E484K, K417T Mutation：D614G, N501Y, E484K, K417T Mutation：D614G, N501Y, E484K, K417T | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 7SXX Cryo-EM structure of the SARS-CoV-2 D614G mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement) Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 7SXY Cryo-EM structure of the SARS-CoV-2 D614G mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Deposited 2021-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 7SXZ Cryo-EM structure of the SARS-CoV-2 D614G,L452R mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement) Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.61 Å |
| 7SY0 Cryo-EM structure of the SARS-CoV-2 D614G,L452R mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Deposited 2021-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7SY1 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement) Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, N501Y Mutation：D614G, N501Y Mutation：D614G, N501Y | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 7SY2 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Deposited 2021-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 7SY3 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement) Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 7SY4 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Deposited 2021-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 7SY5 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement) Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, N501Y, E484K, K417N Mutation：D614G, N501Y, E484K, K417N Mutation：D614G, N501Y, E484K, K417N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.59 Å |
| 7SY6 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417N mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Deposited 2021-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 7SY7 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417T mutant spike protein ectodomain bound to human ACE2 ectodomain (global refinement) Deposited 2021-11-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 7SY8 Cryo-EM structure of the SARS-CoV-2 D614G,N501Y,E484K,K417T mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2) Deposited 2021-11-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 7T01 SARS-CoV-2 S-RBD + Fab 54042-4 Deposited 2021-11-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
329–529（201 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；-4 force, 3 s blot
|
Resolution 2.69 Å |
| 7T3M SARS-CoV-2 S (Spike Glycoprotein) D614G with Three (3) RBDs Up, Bound to Antibody 2-7 scFv, composite map Deposited 2021-12-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: nonameric |
Chain A
1–1149（1149 aa）
Chain C
1–1149（1149 aa）
Chain G
1–1149（1149 aa）
|
Mutation：D614G, R682G, R683S, R685S, K986P, V986P Mutation：D614G, R682G, R683S, R685S, K986P, V986P Mutation：D614G, R682G, R683S, R685S, K986P, V986P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7T67 SARS-CoV-2 S (Spike Glycoprotein) D614G with One(1) RBD Up Deposited 2021-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1149（1149 aa）
Chain C
1–1149（1149 aa）
Chain G
1–1149（1149 aa）
|
Mutation：D614G, R682G, R683S, R685S, K986P, V986P Mutation：D614G, R682G, R683S, R685S, K986P, V986P Mutation：D614G, R682G, R683S, R685S, K986P, V986P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7T72 Epitope-based selection of SARS-CoV-2 neutralizing antibodies from convalescent patients Deposited 2021-12-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–528（196 aa）
Fragment：Receptor Binding Domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Equal volumes (2 uL) of protein solution (~5 mg/ml in 25 mM Tris (pH 8.0), 200 mM NaCl) and well solution (100 mM citrate (pH 4.25), 500 mM LiCl, 13% (w/v) PEG6000) were combined
|
Resolution 3.18 Å R-free 0.308 |
| 7T7B Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing antibody ADI-62113 Fab Deposited 2021-12-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293.15 K；0.08 M sodium acetate pH 4.6, 0.16 M ammonium sulfate, 20% (w/v) polyethylene glycol 4000, and 20% (v/v) glycerol
|
Resolution 2.59 Å R-free 0.267 |
| 7T9J Cryo-EM structure of the SARS-CoV-2 Omicron spike protein Deposited 2021-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 7T9K Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with human ACE2 Deposited 2021-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.45 Å |
| 7T9L Cryo-EM structure of SARS-CoV-2 Omicron spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2021-12-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 7TAS SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (local refinement of the RBD and S2K146) Deposited 2021-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–1208（1208 aa）
|
Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7TAT SARS-CoV-2 spike in complex with the S2K146 neutralizing antibody Fab fragment (two receptor-binding domains open) Deposited 2021-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7TB8 Cryo-EM structure of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 Deposited 2021-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, pH 7.4, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 2-3.5 seconds before plugging.
|
Resolution 2.83 Å |
| 7TBF Locally refined region of SARS-CoV-2 spike in complex with antibodies B1-182.1 and A19-61.1 Deposited 2021-12-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
332–527（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 2-3.5 seconds before plugging.
|
Resolution 3.10 Å |
| 7TC9 Locally refined region of SARS-CoV-2 spike in complex with antibody A19-46.1 Deposited 2021-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
332–526（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 2-3.5 seconds before plugging.
|
Resolution 5.08 Å |
| 7TCA Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibody A19-46.1 Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
14–1205（1192 aa）
Chain B
14–1205（1192 aa）
Chain C
14–1205（1192 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 2-3.5 seconds before plugging.
|
Resolution 3.85 Å |
| 7TCC Cryo-EM structure of SARS-CoV-2 Omicron spike in complex with antibodies A19-46.1 and B1-182.1 Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
14–1205（1192 aa）
Chain B
14–1205（1192 aa）
Chain C
14–1205（1192 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；100 mM HEPES, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 2-3.5 seconds before plugging.
|
Resolution 3.86 Å |
| 7TCQ Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide Deposited 2021-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1148–1157（10 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 11 PEG DI(HYDROXYETHYL)ETHER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M Ammonium sulfate and 30 % PEG400
|
Resolution 2.02 Å R-free 0.213 |
| 7TCQ Crystal structure of SARS-CoV-2 neutralizing antibody WS6 in complex with spike S2 peptide Deposited 2021-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1148–1157（10 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.5 M Ammonium sulfate and 30 % PEG400
|
Resolution 2.02 Å R-free 0.213 |
| 7TE1 SARS-CoV-2 Receptor Binding Domain in Complex with Ab17 Deposited 2022-01-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain D
319–529（211 aa）
Chain E
319–529（211 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291.15 K；0.1 M HEPES pH 7.0 and 30% v/v Jeffamine ED-2001 pH 7.0
|
Resolution 3.50 Å R-free 0.344 |
| 7TEI SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Deposited 2022-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1147（1147 aa）
Chain B
1–1147（1147 aa）
Chain C
1–1147（1147 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7TEW Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2022-01-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1206（1206 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7TEX Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein in complex with human ACE2 Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 7TEY Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.25 Å |
| 7TEZ Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2022-01-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 7TF0 Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein in complex with human ACE2 Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 7TF1 Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein (focused refinement of RBD) Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.57 Å |
| 7TF2 Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 7TF3 Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484A spike protein Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.25 Å |
| 7TF4 Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein (focused refinement of RBD) Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 7TF5 Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) spike protein Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 7TF8 SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Deposited 2022-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1147（1147 aa）
Chain B
1–1147（1147 aa）
Chain C
1–1147（1147 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 7TGW Omicron spike at 3.0 A (open form) Deposited 2022-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7TGX Prototypic SARS-CoV-2 G614 spike (open form) Deposited 2022-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 MAN alpha-D-mannopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7TGY Prototypic SARS-CoV-2 G614 spike (closed form) Deposited 2022-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7THE Structure of RBD directed antibody DH1042 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interface Deposited 2022-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.87 Å |
| 7THK Cryo-EM structure of prefusion SARS-CoV-2 spike omicron B.1.1.529 variant Deposited 2022-01-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1205（1205 aa）
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 7THT CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042 Deposited 2022-01-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain C
27–1147（1121 aa）
Chain S
27–1147（1121 aa）
Chain V
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7TIK Structure of the SARS-CoV-2 Omicron spike post-fusion bundle Deposited 2022-01-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain D
1157–1201（45 aa）
Chain E
1157–1201（45 aa）
Chain F
1157–1201（45 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 7TL1 SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1147（1147 aa）
Chain B
1–1147（1147 aa）
Chain C
1–1147（1147 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7TL9 SARS-CoV-2 Omicron 1-RBD up Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron) Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1147（1147 aa）
Chain B
1–1147（1147 aa）
Chain C
1–1147（1147 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.50 Å |
| 7TLA Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1 Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.13 Å |
| 7TLB Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 2 Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 7TLC Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 1 Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 7TLD Down-state locked, S2 stabilized rS2d-HexaPro SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 2 Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 7TLT SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02 Deposited 2022-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
489–497（9 aa）
Fragment：UNP residues 489-497 (YFPLQSYGF)
|
Not recorded | SO4 SULFATE ION × 3 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.9 M Ammonium Sulfate, 20 mM Magnesium chloride, 0.1M Bis-tris propane, 2% Ethylene glycol, 2% 2-Methyl-2,4-pentanediol
|
Resolution 2.30 Å R-free 0.238 |
| 7TLT SARS-CoV-2 Spike-derived peptide S489-497 (YFPLQSYGF) presented by HLA-A*29:02 Deposited 2022-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
489–497（9 aa）
Fragment：UNP residues 489-497 (YFPLQSYGF)
|
Not recorded | SO4 SULFATE ION × 2 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.9 M Ammonium Sulfate, 20 mM Magnesium chloride, 0.1M Bis-tris propane, 2% Ethylene glycol, 2% 2-Methyl-2,4-pentanediol
|
Resolution 2.30 Å R-free 0.238 |
| 7TLY SARS-CoV-2 S B.1.1.529 Omicron variant (RBD + S309 Local Refinement) Deposited 2022-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
1–145（145 aa）
Chain I
146–212（67 aa）
Chain I
215–1205（991 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7TLZ SARS-CoV-2 S NTD B.1.1.529 Omicron variant + S309 Local Refinement Deposited 2022-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
1–145（145 aa）
Chain J
146–212（67 aa）
Chain J
215–1205（991 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7TM0 SARS-CoV-2 S B.1.1.529 Omicron variant + S309 + S2L20 Global Refinement Deposited 2022-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–145（145 aa）
Chain A
146–212（67 aa）
Chain A
215–1205（991 aa）
Chain B
1–145（145 aa）
Chain B
146–212（67 aa）
Chain B
215–1205（991 aa）
Chain C
1–145（145 aa）
Chain C
146–212（67 aa）
Chain C
215–1205（991 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 50 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7TN0 SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab and S309 Fab Deposited 2022-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain I
324–531（208 aa）
Fragment：Receptor-binding domain
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 CL CHLORIDE ION × 11 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；20% v/v Ethylene glycol, 10% w/v PEG 8000, 0.1 M Tris (base)/BICINE pH 8.5, 0.1 M NDSB-256
|
Resolution 2.85 Å R-free 0.268 |
| 7TN0 SARS-CoV-2 Omicron RBD in complex with human ACE2 and S304 Fab and S309 Fab Deposited 2022-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain S
324–531（208 aa）
Fragment：Receptor-binding domain
|
Not recorded | EDO 1,2-ETHANEDIOL × 7 CL CHLORIDE ION × 10 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；20% v/v Ethylene glycol, 10% w/v PEG 8000, 0.1 M Tris (base)/BICINE pH 8.5, 0.1 M NDSB-256
|
Resolution 2.85 Å R-free 0.268 |
| 7TNW Structural and functional impact by SARS-CoV-2 Omicron spike mutations Deposited 2022-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7TO4 Structural and functional impact by SARS-CoV-2 Omicron spike mutations Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7TOU Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; consensus state D1 Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.24 Å |
| 7TOV Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; consensus state D2 Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 7TOW Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide Deposited 2022-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
808–833（26 aa）
|
Not recorded | CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG3000, 100mM Tris base/HCl pH 7.0, 200mM calcium acetate
|
Resolution 2.15 Å R-free 0.234 |
| 7TOW Antibody DH1058 Fab fragment bound to SARS-CoV-2 fusion peptide Deposited 2022-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
808–833（26 aa）
|
Not recorded | CA CALCIUM ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；20% PEG3000, 100mM Tris base/HCl pH 7.0, 200mM calcium acetate
|
Resolution 2.15 Å R-free 0.234 |
| 7TOX Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D5 state Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 7TOY Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D6 state Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 7TOZ Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D7 state Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.07 Å |
| 7TP0 Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D8 state Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.57 Å |
| 7TP1 Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D9 state Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.81 Å |
| 7TP2 Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D10 state Deposited 2022-01-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 7TP3 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K288.2 Deposited 2022-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Z
319–541（223 aa）
|
Not recorded | CAC CACODYLATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium cacodylate pH 6.5, 40% (v/v) 2-methyl-2,4-pentanediol, and 5% (w/v) polyethylene glycol (PEG) 8000
|
Resolution 2.33 Å R-free 0.231 |
| 7TP4 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody K398.22 Deposited 2022-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Z
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M ammonium formate and 20% (w/v) PEG 3350
|
Resolution 1.95 Å R-free 0.231 |
| 7TP7 Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D11 state Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 7TP8 Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D12 state Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7TP9 Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D13 state Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 7TPA Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D14 state Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7TPC Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D15 state Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.91 Å |
| 7TPE Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D16 state Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7TPF Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 1-RBD-up conformation; Subclassification D17 state Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7TPH Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 2-RBD-up conformation - D3 Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 7TPI SARS-CoV-2 E406W mutant Spike ectodomain Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Fragment：Ectodomain
Chain B
1–1208（1208 aa）
Fragment：Ectodomain
Chain C
1–1208（1208 aa）
Fragment：Ectodomain
|
Mutation：E406W Mutation：E406W Mutation：E406W | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 7TPK SARS-CoV-2 E406W mutant RBD - Local Refinement Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
333–526（194 aa）
Fragment：Receptor-binding domain
|
Mutation：E406W | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7TPL Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the M1 conformation, D4 Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N Mutation：T19R, G142D, R158G, L452R, T478K, D614G, P681R, R682G, R683S, R683S, D950N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.87 Å |
| 7TPR Camel nanobodies 7A3 and 8A2 broadly neutralize SARS-CoV-2 variants Deposited 2022-01-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
15–1159（1145 aa）
Chain B
15–1159（1145 aa）
Chain C
15–1159（1145 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, and residues 682-685 from RRAR to GSAS Mutation：F817P, A892P, A899P, A942P, K986P, V987P, and residues 682-685 from RRAR to GSAS Mutation：F817P, A892P, A899P, A942P, K986P, V987P, and residues 682-685 from RRAR to GSAS | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.39 Å |
| 7TYZ Cryo-EM structure of SARS-CoV-2 spike in complex with FSR22, an anti-SARS-CoV-2 DARPin Deposited 2022-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
Chain E
14–1208（1195 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；10 mM HEPES, 7.4, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.51 Å |
| 7TZ0 Cryo-EM structure of SARS-CoV-2 spike in complex with FSR22, an anti-SARS-CoV-2 DARPin (Local refinement of FSR22 and RBD) Deposited 2022-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
14–1208（1195 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；10 mM HEPES, 7.4, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.17 Å |
| 7U0P SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21F2 Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Wait time 20 seconds and blot time 3 seconds
|
Resolution 3.76 Å |
| 7U0Q SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-02 Deposited 2022-02-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS buffer
cryo-EM vitrification conditions
Cryogen ETHANE；20 second wait time and 3 seconds blot time
|
Resolution 3.86 Å |
| 7U0X SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-13 Deposited 2022-02-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS buffer
cryo-EM vitrification conditions
Cryogen ETHANE；20 second wait time and 3 seconds blot time
|
Resolution 3.82 Å |
| 7U1R SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by HLA-A*02:01 Deposited 2022-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1185–1193（9 aa）
Fragment：RLNEVANNL
|
Mutation：K1191N | CD CADMIUM ION × 1 ZN ZINC ION × 1 NA SODIUM ION × 1 ACT ACETATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；18% P4000, 0.1M HEPES 7.6, 0.1M MgCl2, 1 mM CdCl2
|
Resolution 1.80 Å R-free 0.196 |
| 7U2D Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADG20 Deposited 2022-02-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 5 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.16；293.15 K；0.1 M sodium citrate, pH 4.16 and 1.45 M ammonium sulfate
|
Resolution 2.76 Å R-free 0.259 |
| 7U2E Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody ADI-55688 Deposited 2022-02-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 9 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3.8；293.15 K；0.08 M sodium acetate, pH 3.8, 1.6 M ammonium sulfate, and 20% (v/v) glycerol
|
Resolution 2.85 Å R-free 0.284 |
| 7U8E Crystal structure of antibody Ab246 in complex with SARS-CoV-2 receptor binding domain Deposited 2022-03-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 6 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.6；291 K；0.1 M Sodium acetate trihydrate pH 4.6, 2.0 M Ammonium sulfate
|
Resolution 2.29 Å R-free 0.247 |
| 7U9O SARS-CoV-2 spike trimer RBD in complex with Fab NE12 Deposited 2022-03-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1208（1195 aa）
Fragment：Receptor-binding domain
Chain B
14–1208（1195 aa）
Fragment：Receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7U9P SARS-CoV-2 spike trimer RBD in complex with Fab NA8 Deposited 2022-03-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1208（1195 aa）
Fragment：Receptor-binding domain
Chain B
14–1208（1195 aa）
Fragment：Receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7UAP Structure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1520 Deposited 2022-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7UAQ Structure of the SARS-CoV-2 NTD in complex with C1520, local refinement Deposited 2022-03-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7UAR Structure of the SARS-CoV-2 S 6P trimer in complex with the neutralizing antibody Fab fragment, C1717 Deposited 2022-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7UB0 SARS-CoV-2 Omicron-BA.2 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron-BA.2) Deposited 2022-03-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.31 Å |
| 7UB5 SARS-CoV-2 Omicron-BA.2 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron-BA.2) Deposited 2022-03-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 7UB6 SARS-CoV-2 Omicron-BA.2 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron-BA.2) Deposited 2022-03-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7UHB SARS-CoV-2 spike in complex with AHB2-2GS-SB175 (local refinement of the RBD and AHB2) Deposited 2022-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Mutation：R682,R683,R685,F817,A892,A899,A942,K986,V987 | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7UHC SARS-CoV-2 spike in complex with AHB2-2GS-SB175 Deposited 2022-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Mutation：R682,R683,R685,F817,A892,A899,A942,K986,V987 Mutation：R682,R683,R685,F817,A892,A899,A942,K986,V987 Mutation：R682,R683,R685,F817,A892,A899,A942,K986,V987 | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7UKL Cryo-EM structure of Antibody 12-16 in complex with prefusion SARS-CoV-2 Spike glycoprotein Deposited 2022-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 7UKM Cryo-EM structure of Antibody 12-19 in complex with prefusion SARS-CoV-2 Spike glycoprotein Deposited 2022-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 47 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 7UL0 Crystal structure of SARS-CoV-2 RBD in complex with the ridge-binding nAb EH8 isolated from a nonvaccinated pediatric patient Deposited 2022-04-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；0.2 M sodium chloride, 0.1 M Na HEPES pH 7.5, 12% w/v PEG 8000
|
Resolution 2.49 Å R-free 0.256 |
| 7UL1 Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing IGHV3-53-encoded antibody EH3 isolated from a nonvaccinated pediatric patient Deposited 2022-04-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
329–538（210 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；294 K；0.1M sodium citrate pH 5.0, 8% w/v PEG8000
|
Resolution 2.65 Å R-free 0.221 |
| 7UOW SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 034_32 Deposited 2022-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Wait time 20 seconds and blot time 3 seconds
|
Resolution 4.40 Å |
| 7UPL SARS-Cov2 Omicron varient S protein structure in complex with neutralizing monoclonal antibody 002-S21F2 Deposited 2022-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Wait time 20 seconds and blot time 3 seconds
|
Resolution 4.10 Å |
| 7UPW Three RBD-down state of SARS-CoV-2 D614G spike in complex with the SP1-77 neutralizing antibody Fab fragment Deposited 2022-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å R-free 0.425 |
| 7UPX Three RBD-down state of SARS-CoV-2 D614G spike in complex with the SP1-77 neutralizing antibody Fab fragment (local refinement of the RBD and Fab variable domains) Deposited 2022-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
|
Mutation：D614G | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7UPY An antibody from single human VH-rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion Deposited 2022-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å R-free 0.425 |
| 7URQ Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 1 Deposited 2022-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Mutation：L452R, T478K | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；10% PEG 4000
0.2 M sodium acetate
0.1 M sodium citrate pH 5.5
|
Resolution 2.05 Å R-free 0.208 |
| 7URS Crystal Structure of SARS-CoV-2 S delta variant receptor-binding domain (RBD) in complex CoV11 Fab crystal form 2 Deposited 2022-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Mutation：L452R, T478K | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；12% PEG 8000
0.1 M sodium phosphate pH 6.5
|
Resolution 2.40 Å R-free 0.224 |
| 7UZ4 Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-3 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Fragment：Spike 6P
Chain B
1–1213（1213 aa）
Fragment：Spike 6P
Chain C
1–1213（1213 aa）
Fragment：Spike 6P
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7UZ5 Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-6 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1213（1213 aa）
Fragment：Spike 6P
Chain B
1–1213（1213 aa）
Fragment：Spike 6P
Chain C
1–1213（1213 aa）
Fragment：Spike 6P
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7UZ6 Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-28 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Fragment：Spike 6P
Chain B
1–1213（1213 aa）
Fragment：Spike 6P
Chain C
1–1213（1213 aa）
Fragment：Spike 6P
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7UZ7 Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Fragment：Spike 6P
Chain B
1–1213（1213 aa）
Fragment：Spike 6P
Chain C
1–1213（1213 aa）
Fragment：Spike 6P
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7UZ8 Structure of the SARS-CoV-2 Omicron BA.1 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1212（1212 aa）
Fragment：Omicron BA.1 Spike 6P
Chain B
1–1212（1212 aa）
Fragment：Omicron BA.1 Spike 6P
Chain C
1–1212（1212 aa）
Fragment：Omicron BA.1 Spike 6P
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7UZ9 Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-34 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Fragment：Spike 6P
Chain B
1–1213（1213 aa）
Fragment：Spike 6P
Chain C
1–1213（1213 aa）
Fragment：Spike 6P
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7UZA Structure of the SARS-CoV-2 S 6P trimer in complex with the mouse antibody Fab fragment, HSW-1 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1213（1213 aa）
Fragment：Spike 6P
Chain B
1–1213（1213 aa）
Fragment：Spike 6P
Chain C
1–1213（1213 aa）
Fragment：Spike 6P
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7UZB Structure of the SARS-CoV-2 S S1 doamin in complex with the mouse antibody Fab fragment, HSW-2 Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Fragment：Spike S1 domain
|
Mutation：P817F,P892A,P899A,P942A,P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7UZC Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-34 Deposited 2022-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–533（206 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% v/v tacsimate pH 4.0, 0.1 M sodium acetate trihydrate pH 4.6, 16 % PEG 3350
|
Resolution 2.20 Å R-free 0.243 |
| 7UZC Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, M8a-34 Deposited 2022-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
328–533（206 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% v/v tacsimate pH 4.0, 0.1 M sodium acetate trihydrate pH 4.6, 16 % PEG 3350
|
Resolution 2.20 Å R-free 0.243 |
| 7UZD Structure of the SARS-CoV-2 RBD in complex with the mouse antibody Fab fragment, HSW-2 Deposited 2022-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–533（206 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium chloride, 0.1 M sodium/potassium phosphate pH 6.5, 25 % PEG 1000
|
Resolution 3.00 Å R-free 0.273 |
| 7V20 CryoEM structure of del68-76/del679-688 prefusion-stabilized spike Deposited 2021-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.86 Å |
| 7V22 Local CryoEM structure del68-76/del679-688 prefusion-stabilized spike Deposited 2021-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 7V23 CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9 Deposited 2021-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 7V24 Local CryoEM structure of del68-76/del679-688 prefusion-stabilized spike in complex with the Fab of N12-9 Deposited 2021-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 7V26 XG005-bound SARS-CoV-2 S Deposited 2021-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 7V27 RBD/XG005 local refinement Deposited 2021-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.18 Å |
| 7V2A SARS-CoV-2 Spike trimer in complex with XG014 Fab Deposited 2021-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7V76 Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), uncleavable form, one RBD-up conformation Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.20 Å |
| 7V77 Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), uncleavable form, two RBD-up conformation Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7V78 Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1), one RBD-up conformation 1 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.40 Å |
| 7V79 Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1), one RBD-up conformation 2 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7V7A Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1), two RBD-up conformation Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.40 Å |
| 7V7D Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), all RBD-down conformation Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.00 Å |
| 7V7E Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), one RBD-up conformation 1 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.90 Å |
| 7V7F Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), one RBD-up conformation 2 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.90 Å |
| 7V7G Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), two RBD-up conformation Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.10 Å |
| 7V7H Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 1 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.20 Å |
| 7V7I Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 2 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D Mutation：G142D, E154K, L452R, E484Q, D614G, R682G, R683S, R685S, K986P, V987P, Q107H, H1101D | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7V7J Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1), dimer of S trimer conformation 3 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.40 Å |
| 7V7N Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), all RBD-down conformation Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.90 Å |
| 7V7O Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), one RBD-up conformation 1 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.90 Å |
| 7V7P Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), one RBD-up conformation 2 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.90 Å |
| 7V7Q Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), one RBD-up conformation 3 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.80 Å |
| 7V7R Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), one RBD-up conformation 4 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.90 Å |
| 7V7S Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), one RBD-up conformation 5 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.00 Å |
| 7V7T Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), two RBD-up conformation 1 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.00 Å |
| 7V7U Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), two RBD-up conformation 2 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.00 Å |
| 7V7V Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2), two RBD-up conformation 3 Deposited 2021-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P Mutation：T19R, G142D, E156G, deletion157-158, L452R, T478K, D614G, P681R, R682G, R683S, R685S, D950N, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.10 Å |
| 7V7Z Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R246I, R682G, R683S, R685S, K986P, V987P Mutation：R246I, R682G, R683S, R685S, K986P, V987P Mutation：R246I, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.10 Å |
| 7V80 Local refinement of SARS-CoV-2 S-Beta variant (B.1.351) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R246I, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.90 Å |
| 7V81 Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.20 Å |
| 7V82 Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 1 Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.80 Å |
| 7V83 Cryo-EM structure of SARS-CoV-2 S-Gamma variant (P.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2 Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：G142D, E154K, R682G, R683S, R685S, K986P, V987P Mutation：G142D, E154K, R682G, R683S, R685S, K986P, V987P Mutation：G142D, E154K, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.80 Å |
| 7V84 Local refinement of SARS-CoV-2 S-Gamma variant (P.1) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.00 Å |
| 7V85 Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：E154K, E484Q, R682G, R683S, R685S, K986P, V987P, Q1071H, H1101D Mutation：E154K, E484Q, R682G, R683S, R685S, K986P, V987P, Q1071H, H1101D Mutation：E154K, E484Q, R682G, R683S, R685S, K986P, V987P, Q1071H, H1101D | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7V86 Cryo-EM structure of SARS-CoV-2 S-Kappa variant (B.1.617.1) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：G142D, E154K, R682G, R683S, R685S, K986P, V987P, Q1071H, H1101D Mutation：G142D, E154K, R682G, R683S, R685S, K986P, V987P, Q1071H, H1101D Mutation：G142D, E154K, R682G, R683S, R685S, K986P, V987P, Q1071H, H1101D | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.80 Å |
| 7V87 Local refinement of SARS-CoV-2 S-Kappa variant (B.1.617.1) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain Deposited 2021-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7V88 Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, two ACE2-bound form Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.30 Å |
| 7V89 Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 1 Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.80 Å |
| 7V8A Cryo-EM structure of SARS-CoV-2 S-Delta variant (B.1.617.2) in complex with Angiotensin-converting enzyme 2 (ACE2) ectodomain, three ACE2-bound form conformation 2 Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 2.70 Å |
| 7V8B Local refinement of SARS-CoV-2 S-Delta variant (B.1.617.2) RBD and Angiotensin-converting enzyme 2 (ACE2) ectodomain Deposited 2021-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.20 Å |
| 7V8C Cryo-EM structure of SARS-CoV-2 S-Beta variant (B.1.351), Cleavable form, one RBD-up conformation Deposited 2021-08-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 2.5 seconds before plunging; blot force: 0; waiting time: 30s
|
Resolution 3.40 Å |
| 7VHH Delta variant of SARS-CoV-2 Spike protein Deposited 2021-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1148（1135 aa）
Chain B
14–1148（1135 aa）
Chain C
14–1148（1135 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.45
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7VHJ Furin Site deletion of SARS-CoV-2 spike Deposited 2021-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7VHK S1-S2 deletion S-2P trimer(3 down) Deposited 2021-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7VHL Double deletion S-2P trimer(1 Up) Deposited 2021-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7VHM Double deletion S-2P trimer(3 down) Deposited 2021-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7VHN Spike of SARS-CoV-2 spike protein(1 up) Deposited 2021-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1148（1135 aa）
Chain B
14–1148（1135 aa）
Chain C
14–1148（1135 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7VMU Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody Deposited 2021-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
335–515（181 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；20% w/v PEG3350, 0.2M potassium citrate tribasic
|
Resolution 2.89 Å R-free 0.273 |
| 7VNB Crystal structure of the SARS-CoV-2 RBD in complex with a human single domain antibody n3113 Deposited 2021-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–531（213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；4.3M sodium chloride and 0.1M HEPES, pH 7.5
|
Resolution 2.27 Å R-free 0.203 |
| 7VNC Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain antibody n3113 (UDD-state, state 1) Deposited 2021-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7VND Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain antibody n3113 (UUD-state, state 2) Deposited 2021-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7VNE Structure of the SARS-CoV-2 spike glycoprotein in complex with a human single domain antibody n3113.1 (UUU-state) Deposited 2021-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P Mutation：R682G,R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7VOA Crystal structure of SARS-CoV-2 RBD in complex with aRBD5 Deposited 2021-10-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
321–528（208 aa）
Fragment：UNP residues 321-528
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；0.1M Sodium cacodylate pH 5.5, 25%(w/v) PEG 4000
|
Resolution 1.80 Å R-free 0.226 |
| 7VQ0 Cryo-EM structure of the SARS-CoV-2 spike protein (2-up RBD) bound to neutralizing nanobodies P86 Deposited 2021-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G, R682G, R683S, R685S, K986P, V987P Mutation：D614G, R682G, R683S, R685S, K986P, V987P Mutation：D614G, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 7VRV VAS5 Spike (1 RBD up) Deposited 2021-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
13–1213（1201 aa）
Chain B
13–1213（1201 aa）
Chain C
13–1213（1201 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7VRW VAS5 Spike (3 RBD down) Deposited 2021-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
13–1213（1201 aa）
Chain B
13–1213（1201 aa）
Chain C
13–1213（1201 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7VX1 SARS-CoV-2 Beta variant spike protein in open state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7VX4 ACE2-RBD in SARS-CoV-2 Beta variant S-ACE2 complex Deposited 2021-11-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–1206（1206 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7VX5 ACE2-RBD in SARS-CoV-2 Kappa variant S-ACE2 complex Deposited 2021-11-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–1208（1208 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7VX9 SARS-CoV-2 Kappa variant spike protein in complex wth ACE2, state C1 Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1146（1133 aa）
Chain B
14–1146（1133 aa）
Chain D
14–1146（1133 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7VXA SARS-CoV-2 Kappa variant spike protein in complex with ACE2, state C2a Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7VXB SARS-CoV-2 Kappa variant spike protein in C2b state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7VXC SARS-CoV-2 Kappa variant spike protein in C3 state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7VXD SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C1 state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain D
1–1206（1206 aa）
|
Mutation：deletions 241-243 Mutation：deletions 241-243 Mutation：deletions 241-243 | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7VXE SARS-CoV-2 Kappa variant spike protein in open state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7VXF SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C2B state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain D
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7VXI SARS-CoV-2 Kappa variant spike protein in transition state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7VXK SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C2A state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain D
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7VXM SARS-CoV-2 spike protein in complex with ACE2, Beta variant, C3 state Deposited 2021-11-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain D
1–1206（1206 aa）
|
Mutation：deletions 241-243 Mutation：deletions 241-243 Mutation：deletions 241-243 | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7VYR Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody Fab fragment Deposited 2021-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；20% (v/v) PEG 3350, 200mM NH4Cl
|
Resolution 2.20 Å R-free 0.235 |
| 7VYR Crystal structure of SARS-CoV-2 Spike RBD in complex with the D27 neutralizing antibody Fab fragment Deposited 2021-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293.15 K；20% (v/v) PEG 3350, 200mM NH4Cl
|
Resolution 2.20 Å R-free 0.235 |
| 7VZT A human neutralizing antibody targeting SARS-CoV-2 RBD Deposited 2021-11-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–532（200 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；100mM HEPES (pH 7.5), 40% (v/v) Polyethylene glycol monomethyl ether 400
|
Resolution 3.41 Å R-free 0.263 |
| 7W1S Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-007 Deposited 2021-11-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
320–537（218 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 20% w/v Polyethylene glycol 3350, pH 6.9
|
Resolution 2.00 Å R-free 0.224 |
| 7W6U Structure of SARS-CoV-2 spike receptor-binding domain complexed with its receptor equine ACE2 Deposited 2021-12-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：UNP residues 319-541
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；10% (w/v) PEG 1000, 10% (w/v) PEG 8000
|
Resolution 2.56 Å R-free 0.227 |
| 7W8S Structure of SARS-CoV-2 spike receptor-binding domain Y453F mutation complexed with American mink ACE2 Deposited 2021-12-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：Y453F
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 7W92 Open state of SARS-CoV-2 Delta variant spike protein Deposited 2021-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7W94 Transition state of SARS-CoV-2 Delta variant spike protein Deposited 2021-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7W98 SARS-CoV-2 Delta S-ACE2-C1 Deposited 2021-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7W99 SARS-CoV-2 Delta S-ACE2-C2a Deposited 2021-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
Chain D
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7W9B SARS-CoV-2 Delta S-ACE2-C2b Deposited 2021-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
Chain D
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7W9C SARS-CoV-2 Delta S-ACE2-C3 Deposited 2021-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
Chain D
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7W9E SARS-CoV-2 Delta S-8D3 Deposited 2021-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7W9F SARS-CoV-2 Delta S-RBD-8D3 Deposited 2021-12-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7W9I SARS-CoV-2 Delta S-RBD-ACE2 Deposited 2021-12-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WA1 Structure of SARS-CoV-2 spike receptor-binding domain F486L mutation complexed with American mink ACE2 Deposited 2021-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Mutation：F486L | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7WBH overall structure of hu33 and spike Deposited 2021-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1146（1120 aa）
Chain B
27–1146（1120 aa）
Chain C
27–1146（1120 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7WBL Cryo-EM structure of human ACE2 complexed with SARS-CoV-2 Omicron RBD Deposited 2021-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WBP Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with its receptor human ACE2 Deposited 2021-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES pH 6.5,10%w/v PEG 5000 MME,12% v/v 1-propanol
|
Resolution 3.00 Å R-free 0.204 |
| 7WBQ Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike glycoprotein in complex with its receptor human ACE2 Deposited 2021-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES pH 6.5,10%w/v PEG 5000 MME,12% v/v 1-propanol
|
Resolution 3.34 Å R-free 0.226 |
| 7WBQ Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike glycoprotein in complex with its receptor human ACE2 Deposited 2021-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；0.1M MES pH 6.5,10%w/v PEG 5000 MME,12% v/v 1-propanol
|
Resolution 3.34 Å R-free 0.226 |
| 7WBZ Crystal structure of the SARS-Cov-2 RBD in complex with Fab 2303 Deposited 2021-12-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；309 K；0.2 M sodium tartrate dibasic dihydrate, 14% (w/v) polyethylene glycol 3350
|
Resolution 2.42 Å R-free 0.220 |
| 7WCD Cryo EM structure of SARS-CoV-2 spike in complex with TAU-2212 mAbs in conformation 4 Deposited 2021-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain C
1–1208（1208 aa）
Chain H
1–1208（1208 aa）
Chain J
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S,K986P,V987P Mutation：R682G, R683S, R685S,K986P,V987P Mutation：R682G, R683S, R685S,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7WCR RBD-1 of SARS-CoV-2 Beta spike in complex with S5D2 Fab Deposited 2021-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WCZ SARS-CoV-2 Beta spike in complex with one S5D2 Fab Deposited 2021-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WD0 SARS-CoV-2 Beta spike in complex with two S5D2 Fabs Deposited 2021-12-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7WD1 Crystal structure of R14 bound to SARS-CoV-2 RBD Deposited 2021-12-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.10% w/v n-Octyl-b-D-glucoside, 0.1M Sodium citrate tribasic dihydrate (pH 5.5), 22% w/v Polyethylene glycol 3350
|
Resolution 2.50 Å R-free 0.239 |
| 7WD1 Crystal structure of R14 bound to SARS-CoV-2 RBD Deposited 2021-12-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.10% w/v n-Octyl-b-D-glucoside, 0.1M Sodium citrate tribasic dihydrate (pH 5.5), 22% w/v Polyethylene glycol 3350
|
Resolution 2.50 Å R-free 0.239 |
| 7WD2 Crystal structure of S43 bound to SARS-CoV-2 RBD Deposited 2021-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–530（198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium sulfate, 0.1M Tris (pH 8.5), 30% w/v PEG 4000
|
Resolution 2.69 Å R-free 0.229 |
| 7WD2 Crystal structure of S43 bound to SARS-CoV-2 RBD Deposited 2021-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Lithium sulfate, 0.1M Tris (pH 8.5), 30% w/v PEG 4000
|
Resolution 2.69 Å R-free 0.229 |
| 7WD7 SARS-CoV-2 Beta spike in complex with three S5D2 Fabs Deposited 2021-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WD8 SARS-CoV-2 Beta spike SD1 in complex with S3H3 Fab Deposited 2021-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7WD9 SARS-CoV-2 Beta spike in complex with three S3H3 Fabs Deposited 2021-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7WDF SARS-CoV-2 Beta spike in complex with two S3H3 Fabs Deposited 2021-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7WE7 SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv282 Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain D
1–1273（1273 aa）
Chain E
1–1273（1273 aa）
Chain G
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7WE8 SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv265 Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WE9 SARS-CoV-2 Omicron variant spike protein in complex with Fab XGv289 Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain F
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7WEA SARS-CoV-2 Omicron variant spike protein in complex with two XGv347 binding to one close state RBD and one open state RBD Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：deletions Mutation：deletions Mutation：deletions | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7WEB SARS-CoV-2 Omicron variant spike protein with two XGv347 binding to two open state RBDs Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
Chain D
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7WEC SARS-CoV-2 Omicron variant spike protein with three XGv347 Fabs binding to three closed state RBDs Deposited 2021-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7WED SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv347 Deposited 2021-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–530（201 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WEE SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv265 Deposited 2021-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7WEF SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv289 Deposited 2021-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–530（201 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7WEV SARS-COV-2 BETA VARIANT SPIKE PROTEIN IN TRANSITION STATE Deposited 2021-12-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7WG6 Neutral Omicron Spike Trimer Deposited 2021-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1162（1149 aa）
Chain B
14–1162（1149 aa）
Chain C
14–1162（1149 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WG7 Acidic Omicron Spike Trimer Deposited 2021-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7WG8 Delta Spike Trimer(3 RBD Down) Deposited 2021-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1148（1135 aa）
Chain B
14–1148（1135 aa）
Chain C
14–1148（1135 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7WG9 Delta Spike Trimer(1 RBD Up) Deposited 2021-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WGB Neutral Omicron Spike Trimer in complex with ACE2 Deposited 2021-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WGC Neutral Omicron Spike Trimer in complex with ACE2. Deposited 2021-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7WGV SARS-CoV-2 spike glycoprotein trimer in closed state Deposited 2021-12-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 EIC LINOLEIC ACID × 3 BLR 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7WGX SARS-CoV-2 spike glycoprotein trimer in closed state after treatment with Cathepsin L Deposited 2021-12-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 BLR 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WGY SARS-CoV-2 spike glycoprotein trimer in Intermediate state Deposited 2021-12-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7WGZ SARS-CoV-2 spike glycoprotein trimer in open state Deposited 2021-12-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 7WH8 SARS-CoV-2 spike in complex with the ZB8 neutralizing antibody Fab (focused refinement on Fab-RBD) Deposited 2021-12-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
317–593（277 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 7WHB SARS-CoV-2 spike in complex with the ZB8 neutralizing antibody Fab (3U) Deposited 2021-12-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1146（1120 aa）
Chain B
27–1146（1120 aa）
Chain C
27–1146（1120 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.67 Å |
| 7WHD SARS-CoV-2 spike in complex with the ZB8 neutralizing antibody Fab (2u1d) Deposited 2021-12-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
27–1146（1120 aa）
Chain B
27–1146（1120 aa）
Chain C
27–1146（1120 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 7WHH Crystal structure of SARS-CoV-2 omicron RBD and human ACE2 Deposited 2021-12-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
Fragment：Omicron RBD
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10% w/v Polyethylene glycol 3350
|
Resolution 2.60 Å R-free 0.231 |
| 7WHI The state 2 complex structure of Omicron spike with Bn03 (2-up RBD, 4 nanobodies) Deposited 2021-12-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 7WHJ The state 1 complex structure of Omicron spike with Bn03 (1-up RBD, 3 nanobodies) Deposited 2021-12-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 40 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 7WHK The state 3 complex structure of Omicron spike with Bn03 (2-up RBD, 5 nanobodies) Deposited 2021-12-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 7WHZ SARS-CoV-2 spike protein in complex with three human neutralizing antibodies Deposited 2022-01-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 7WI0 SARS-CoV-2 Omicron variant spike in complex with three human neutralizing antibodies Deposited 2022-01-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.82 Å |
| 7WJY Omicron spike trimer with 6m6 antibody Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain G
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.24 Å |
| 7WJZ Omicron Spike bitrimer with 6m6 antibody Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain B
1–1208（1208 aa）
Chain I
1–1208（1208 aa）
Chain J
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
Chain L
1–1208（1208 aa）
Chain M
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 49 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 7WK0 Local refine of Omicron spike bitrimer with 6m6 antibody Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
331–528（198 aa）
Fragment：RBD
Chain F
331–528（198 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 7WK2 SARS-CoV-2 Omicron S-close Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7WK3 SARS-CoV-2 Omicron S-open Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WK4 Cryo-EM structure of SARS-CoV-2 Omicron spike protein with ACE2, C1 state Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
Chain D
1–1205（1205 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 7WK5 Cryo-EM structure of Omicron S-ACE2, C2 state Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
Chain D
1–1205（1205 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 7WK6 Cryo-EM structure of SARS-CoV-2 Omicron spike protein with human ACE2 (focus refinement on RBD-1/ACE2) Deposited 2022-01-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 7WK8 SARS-CoV-2 Omicron spike protein SD1 in complex with S3H3 Fab Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.61 Å |
| 7WK9 SARS-CoV-2 Omicron open state spike protein in complex with S3H3 Fab Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 7WKA SARS-CoV-2 Omicron closed state spike protein in complex with S3H3 Fab Deposited 2022-01-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.64 Å |
| 7WLC SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv282 Deposited 2022-01-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–530（201 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7WLY Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down- and 2 up RBDs) Deposited 2022-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WLZ Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down-, 1 up- and 1 invisible RBDs) Deposited 2022-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 7WM0 Cryo-EM structure of the Omicron RBD in complex with 35B5 Fab( local refinement of the RBD and 35B5 Fab) Deposited 2022-01-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 7WN2 Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab Deposited 2022-01-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
321–536（216 aa）
Fragment：Receptor-binding domain
|
Not recorded | SO4 SULFATE ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.25 M ammonium sulfate, 22.5% PEG3350, 0.1 M MES pH 6.0
|
Resolution 2.35 Å R-free 0.279 |
| 7WN2 Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab Deposited 2022-01-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
321–536（216 aa）
Fragment：Receptor-binding domain
|
Not recorded | SO4 SULFATE ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.25 M ammonium sulfate, 22.5% PEG3350, 0.1 M MES pH 6.0
|
Resolution 2.35 Å R-free 0.279 |
| 7WNB Crystal structure of SARS-CoV-2 spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab Deposited 2022-01-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
321–536（216 aa）
Fragment：Receptor-binding domain
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.5 M ammonium sulfate, 19% PEG3350, 0.1 M Bis-Tris pH 5.5
|
Resolution 2.18 Å R-free 0.281 |
| 7WNM Structure of SARS-CoV-2 Gamma variant receptor-binding domain complexed with high affinity human ACE2 mutant (T27F,R273Q) Deposited 2022-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–541（223 aa）
Fragment：Receptor-binding domain
|
Mutation：N501Y | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M magnesium chloride, 0.1 M MES (pH 6.0) and 8% w/v polyethylene glycol 6000
|
Resolution 2.70 Å R-free 0.223 |
| 7WO4 SARS-CoV-2 Spike in complex with IgG 553-15 (S-553-15 dimer trimer ) Deposited 2022-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain J
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
Chain L
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 90 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.47 Å |
| 7WO5 SARS-CoV-2 Spike in complex with IgG 553-15 (S-553-15 trimer) Deposited 2022-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 7WO7 Locally refined region of SARS-CoV-2 Spike in complex with IgG 553-15 Deposited 2022-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7WOA SARS-CoV-2 Spike in complex with IgG 553-60 (1-up trimer) Deposited 2022-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 7WOB SARS-CoV-2 Spike in complex with IgG 553-60 (2-up trimer) Deposited 2022-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 7WOC Locally refined region of SARS-CoV-2 Spike in complex with IgG 553-60 Deposited 2022-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 7WOG SARS-CoV-2 Omicron S monomer complexed with 553-49 Deposited 2022-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
331–528（198 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.06 Å |
| 7WON Cryo-EM structure of SARS-CoV-2 S2P trimer in complex with neutralizing antibody VacW-209 (local refinement) Deposited 2022-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–521（189 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7WOP The local refined map of Omicron spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–528（198 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.51 Å |
| 7WOQ The state 1 of Omicron Spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 7WOR The state 2 of Omicron Spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7WOS The state 3 of Omicron Spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.91 Å |
| 7WOU The state 4 of Omicron Spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 7WOV The state 5 of Omicron Spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.87 Å |
| 7WOW The state 6 of Omicron Spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.11 Å |
| 7WOW The state 6 of Omicron Spike with bispecific antibody FD01 Deposited 2022-01-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain J
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
Chain L
1–1208（1208 aa）
|
Mutation：hexaPro mutations Mutation：hexaPro mutations Mutation：hexaPro mutations | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.11 Å |
| 7WP0 Cryo-EM structure of SARS-CoV-2 Delta S6P trimer in complex with neutralizing antibody VacW-209 (local refinement) Deposited 2022-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–521（189 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.71 Å |
| 7WP1 Cryo-EM structure of SARS-CoV-2 Mu S6P trimer in complex with neutralizing antibody VacW-209 (local refinement) Deposited 2022-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–521（189 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.77 Å |
| 7WP2 Cryo-EM structure of SARS-CoV-2 C.1.2 S6P trimer in complex with neutralizing antibody VacW-209 (local refinement) Deposited 2022-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–521（189 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7WP5 Cryo-EM structure of SARS-CoV-2 Omicron S6P trimer in complex with neutralizing antibody VacW-209 (local refinement) Deposited 2022-01-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–521（189 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7WP6 Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK in complex with three neutralizing antibodies Deposited 2022-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain F
333–521（189 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.81 Å |
| 7WP8 Cryo-EM structure of SARS-CoV-2 recombinant spike protein STFK1628x in complex with three neutralizing antibodies Deposited 2022-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain F
336–518（183 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.88 Å |
| 7WP9 SARS-CoV-2 Omicron Variant SPIKE trimer, all RBDs down Deposited 2022-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.56 Å |
| 7WPA SARS-CoV-2 Omicron Variant SPIKE trimer complexed with ACE2 Deposited 2022-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 CL CHLORIDE ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 7WPB SARS-CoV-2 Omicron Variant RBD complexed with ACE2 Deposited 2022-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R684S, R685S, K989P, V990P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 7WPC The second RBD of SARS-CoV-2 Omicron Variant in complexed with RBD-ACE2 Deposited 2022-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
|
Not recorded | CL CHLORIDE ION × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.57 Å |
| 7WPD SARS-CoV-2 Omicron Variant S Trimer complexed with one JMB2002 Fab Deposited 2022-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 3.18 Å |
| 7WPE SARS-CoV-2 Omicron Variant S Trimer complexed with two JMB2002 Fab Deposited 2022-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：Q498R, R682G, R683S, R685S, K986P, V987P Mutation：Q498R, R682G, R683S, R685S, K986P, V987P Mutation：Q498R, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.69 Å |
| 7WPF SARS-CoV-2 Omicron Variant S Trimer complexed with three JMB2002 Fab Deposited 2022-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：Q498R, R682G, R683S, R685S, K986P, V987P Mutation：Q498R, R682G, R683S, R685S, K986P, V987P Mutation：Q498R, R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.92 Å |
| 7WPH SARS-CoV2 RBD bound to Fab06 Deposited 2022-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–591（273 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M magnesium formate dihydrate, 20% w/v PEG 3350
|
Resolution 2.89 Å R-free 0.269 |
| 7WPH SARS-CoV2 RBD bound to Fab06 Deposited 2022-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–591（273 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M magnesium formate dihydrate, 20% w/v PEG 3350
|
Resolution 2.89 Å R-free 0.269 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
330–531（202 aa）
Fragment：RBD
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
330–531（202 aa）
Fragment：RBD
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
330–531（202 aa）
Fragment：RBD
|
Not recorded | CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
330–531（202 aa）
Fragment：RBD
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
330–531（202 aa）
Fragment：RBD
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain K
330–531（202 aa）
Fragment：RBD
|
Not recorded | CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
330–531（202 aa）
Fragment：RBD
|
Not recorded | CA CALCIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WQV Crystal structure of a neutralizing monoclonal antibody (Ab08) in complex with SARS-CoV-2 receptor-binding domain (RBD) Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain O
330–531（202 aa）
Fragment：RBD
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Magnesium chloride hexahydrate, calcium chloride dihydrate, sodium HEPES, MOPS (acid), MPD, PEG 1000, PEG 3350
|
Resolution 2.80 Å R-free 0.251 |
| 7WR8 Local CryoEM structure of the SARS-CoV-2 S6P(B.1.1.529) in complex with BD55-3152 Fab Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WRH Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2 Deposited 2022-01-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
15–1208（1194 aa）
Chain B
15–1208（1194 aa）
Chain C
15–1208（1194 aa）
|
Mutation：F817P, A892P, A899P, A942P Mutation：F817P, A892P, A899P, A942P Mutation：F817P, A892P, A899P, A942P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 7WRI Cryo-EM structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with mouse ACE2 Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
14–1205（1192 aa）
Fragment：UNP residues 14-1205
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 7WRJ Local CryoEM structure of the SARS-CoV-2 S6P(B.1.1.529) in complex with BD55-4637 Fab Deposited 2022-01-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.08 Å |
| 7WRL Local structure of BD55-1239 Fab and SARS-COV2 Omicron RBD complex Deposited 2022-01-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.51 Å |
| 7WRO Local structure of BD55-3372 and delta spike Deposited 2022-01-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
334–516（183 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WRV The interface of JMB2002 Fab binds to SARS-CoV-2 Omicron Variant S Deposited 2022-01-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R684G, R685G, K989P, V990P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.47 Å |
| 7WRY Local structure of BD55-3546 Fab and SARS-COV2 Delta RBD complex Deposited 2022-01-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.28 Å |
| 7WRZ Local resolution of BD55-5840 Fab and SARS-COV2 Omicron RBD Deposited 2022-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
335–527（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.26 Å |
| 7WS0 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7WS1 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WS2 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–530（200 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7WS3 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7WS4 Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants Deposited 2022-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：deletion (H69-V70,V143-Y145), insertion(214 EPE) Mutation：deletion (H69-V70,V143-Y145), insertion(214 EPE) Mutation：deletion (H69-V70,V143-Y145), insertion(214 EPE) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7WS5 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：RRAR(682-685)GSAS, K986P, V987P Mutation：RRAR(682-685)GSAS, K986P, V987P Mutation：RRAR(682-685)GSAS, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7WS6 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–536（218 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7WS7 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
326–530（205 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WS8 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7WS9 Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7WSA Structures of Omicron Spike complexes illuminate broad-spectrum neutralizing antibody development Deposited 2022-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
330–530（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7WSC Local structure of BD55-3500 and omicron RBD complex Deposited 2022-01-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.78 Å |
| 7WSE Cryo-EM structure of SARS-CoV-2 spike receptor-binding domain complexed with its receptor minke whale ACE2 Deposited 2022-01-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 7WSH Cryo-EM structure of SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2 Deposited 2022-01-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 7WSK Crystal structure of SARS-CoV-2 Omicron spike receptor-binding domain in complex with civet ACE2 Deposited 2022-01-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Potassium thiocyanate, 20% w/v Polyethylene glycol 3,350
|
Resolution 3.30 Å R-free 0.275 |
| 7WT7 SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 1) Deposited 2022-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 41 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WT8 SARS-CoV-2 Omicron variant spike in complex with Fab 9A8 (State 2) Deposited 2022-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7WT9 SARS-CoV-2 Omicron variant spike RBD in complex with Fab 9A8 Deposited 2022-02-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
1–1273（1273 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7WTF SARS-CoV-2 Omicron variant spike in complex with Fab XGv051 Deposited 2022-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain B
14–1162（1149 aa）
Chain C
14–1162（1149 aa）
Chain D
14–1162（1149 aa）
|
Mutation：deletion, insersion, K986P, V987P Mutation：deletion, insersion, K986P, V987P Mutation：deletion, insersion, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7WTG SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv051 Deposited 2022-02-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–530（201 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7WTH SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv264 Deposited 2022-02-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–530（201 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7WTI SARS-CoV-2 Omicron variant spike in complex with Fab XGv264 Deposited 2022-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7WTJ SARS-CoV-2 Omicron variant spike RBD in complex with Fab XGv286 Deposited 2022-02-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–530（201 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7WTK SARS-CoV-2 Omicron variant spike in complex with Fab XGv286 Deposited 2022-02-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1162（1149 aa）
Chain B
14–1162（1149 aa）
Chain C
14–1162（1149 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7WUE Crystal structure of SARS-CoV-2 Receptor Binding Domain in complex with the monoclonal antibody m31A7 Deposited 2022-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；2.0 M Ammonia sulfate, 0.1M sodium acetate pH 4.6
|
Resolution 3.20 Å R-free 0.295 |
| 7WUE Crystal structure of SARS-CoV-2 Receptor Binding Domain in complex with the monoclonal antibody m31A7 Deposited 2022-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–527（195 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；293.15 K；2.0 M Ammonia sulfate, 0.1M sodium acetate pH 4.6
|
Resolution 3.20 Å R-free 0.295 |
| 7WUH SARS-CoV-2 Spike in complex with Fab of m31A7 Deposited 2022-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
Chain E
14–1208（1195 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.70 Å |
| 7WVL Structure of P4A2 Fab in complex with Spike-RBD from SARS-CoV-2 Deposited 2022-02-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
332–532（201 aa）
Fragment：Receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；20% Peg 5K MME, 0.2 M Magnesium formate
|
Resolution 3.00 Å R-free 0.279 |
| 7WVN SARS-CoV-2 Omicron S-open Deposited 2022-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1205（1205 aa）
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WVO SARS-CoV-2 Omicron S-open-2 Deposited 2022-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1205（1205 aa）
Chain B
1–1205（1205 aa）
Chain C
1–1205（1205 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 7WVP Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C2 state Deposited 2022-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7WVQ Cryo-EM structure of SARS-CoV-2 Omicron Spike protein with human ACE2 receptor, C3 state Deposited 2022-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.04 Å |
| 7WWI SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab in the class 1 conformation Deposited 2022-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WWJ SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab in the class 2 conformation Deposited 2022-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7WWK Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab Deposited 2022-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
334–527（194 aa）
Chain C
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WWL S protein of Delta variant in complex with ZWD12 Deposited 2022-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：Six proline substitutions at residues 817, 892, 899, 942, 986, and 987 Mutation：Six proline substitutions at residues 817, 892, 899, 942, 986, and 987 Mutation：Six proline substitutions at residues 817, 892, 899, 942, 986, and 987 | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7WWM S protein of Delta variant in complex with ZWC6 Deposited 2022-02-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：Six proline substitutions at residues 817, 892, 899, 942, 986, and 987 Mutation：Six proline substitutions at residues 817, 892, 899, 942, 986, and 987 Mutation：Six proline substitutions at residues 817, 892, 899, 942, 986, and 987 | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7WXZ Crystal structure of the recombinant protein HR121 from the S2 protein of SARS-CoV-2 Deposited 2022-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
912–988（77 aa）
Chain A
1163–1206（44 aa）
Chain B
912–988（77 aa）
Chain B
1163–1206（44 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2M sodium fluoride, 20% w/v Polyethylene glycol 3350
|
Resolution 2.41 Å R-free 0.294 |
| 7WXZ Crystal structure of the recombinant protein HR121 from the S2 protein of SARS-CoV-2 Deposited 2022-02-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
912–988（77 aa）
Chain C
1163–1206（44 aa）
Chain D
912–988（77 aa）
Chain D
1163–1206（44 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2M sodium fluoride, 20% w/v Polyethylene glycol 3350
|
Resolution 2.41 Å R-free 0.294 |
| 7WZ1 SARS-CoV-2 Omicron Spike trimer Deposited 2022-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7WZ2 SARS-CoV-2 (D614G) Spike trimer Deposited 2022-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7X08 S protein of SARS-CoV-2 in complex with 2G1 Deposited 2022-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 7X1M The complex structure of Omicron BA.1 RBD with BD604, S309,and S304 Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain M
333–541（209 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.74 Å |
| 7X2H Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with 6-2C Fab Deposited 2022-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
334–528（195 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1M BIS-TRIS pH 6.5, 16% w/v Polyethylene glycol 10000
|
Resolution 2.10 Å R-free 0.269 |
| 7X2H Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with 6-2C Fab Deposited 2022-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
334–528（195 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1M BIS-TRIS pH 6.5, 16% w/v Polyethylene glycol 10000
|
Resolution 2.10 Å R-free 0.269 |
| 7X2K Crystal structure of nanobody Nb70 with antibody 1F11 fab and SARS-CoV-2 RBD Deposited 2022-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–526（194 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15M DL-Malic acid pH 7.0, 20% w/v Polyethylene glycol 3350
|
Resolution 2.40 Å R-free 0.245 |
| 7X2L Crystal structure of nanobody 3-2A2-4 with SARS-CoV-2 RBD Deposited 2022-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–528（196 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1M DL-Malic acid pH7.0, 12% w/v Polyethylene glycol 3350
|
Resolution 2.40 Å R-free 0.287 |
| 7X2M Crystal structure of nanobody 1-2C7 with SARS-CoV-2 RBD Deposited 2022-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–529（197 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M Ammonium sulfate, 0.1M Bis Tris pH 5.5, 25% w/v Polyethylene glycol 3350
|
Resolution 1.80 Å R-free 0.207 |
| 7X63 SARS-CoV-2-Beta-RBD and BD-236-GWP/P-VK antibody complex Deposited 2022-03-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；4% v/v Tacsimate pH 8.0, 12% w/v Polyethylene Glycol 3350
|
Resolution 2.24 Å R-free 0.224 |
| 7X66 SARS-CoV-2-Omicron-RBD and BD-236-GWP/P-VK antibody complex Deposited 2022-03-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–528（210 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；4% v/v Tacsimate pH 6.0, 12% w/v Polyethylene Glycol 3350
|
Resolution 2.40 Å R-free 0.238 |
| 7X6A SARS-CoV-2 BA.2 variant spike protein in complex with Fab BD55-5840 Deposited 2022-03-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain D
1–1273（1273 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7X7D SARS-CoV-2 Delta RBD and Nb22 Deposited 2022-03-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
334–527（194 aa）
Fragment：Delta RBD
Chain D
334–527（194 aa）
Fragment：Delta RBD
Chain E
334–527（194 aa）
Fragment：Delta RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；0.1 M Tris (pH 7.0), 37.5% Jeffamine
|
Resolution 2.92 Å R-free 0.256 |
| 7X7E SARS-CoV-2 RBD and Nb22 Deposited 2022-03-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
334–527（194 aa）
Chain D
334–527（194 aa）
Chain F
334–527（194 aa）
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；0.1 M HEPES (pH 480 7.0), 5% MPD, 10% PEG 10000
|
Resolution 2.67 Å R-free 0.249 |
| 7X7N 3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of synthetic peptide SIH-5. Deposited 2022-03-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.47 Å |
| 7X7O SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K Deposited 2022-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
322–536（215 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Citric acid pH5.0, 1.0 M Lithium chloride, 10% (w/v) PEG 6000
|
Resolution 3.75 Å R-free 0.336 |
| 7X7O SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K Deposited 2022-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
322–536（215 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Citric acid pH5.0, 1.0 M Lithium chloride, 10% (w/v) PEG 6000
|
Resolution 3.75 Å R-free 0.336 |
| 7X7O SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K Deposited 2022-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
322–536（215 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Citric acid pH5.0, 1.0 M Lithium chloride, 10% (w/v) PEG 6000
|
Resolution 3.75 Å R-free 0.336 |
| 7X7O SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K Deposited 2022-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
322–536（215 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Citric acid pH5.0, 1.0 M Lithium chloride, 10% (w/v) PEG 6000
|
Resolution 3.75 Å R-free 0.336 |
| 7X7T Cryo-EM structure of SARS-CoV-2 spike protein in complex with three nAbs X01, X10 and X17 Deposited 2022-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain G
324–527（204 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 7X7U Cryo-EM structure of SARS-CoV-2 Delta variant spike protein in complex with three nAbs X01, X10 and X17 Deposited 2022-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain G
324–527（204 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.77 Å |
| 7X8W The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab354 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7X8Y The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab159 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7X8Z The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab188 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7X90 The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab326 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7X91 The SARS-CoV-2 receptor binding domain bound with an Fv-clasp form of a human neutralizing antibody Ab496 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 7X92 The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab445 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7X93 The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab765 Deposited 2022-03-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain G
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7X94 The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab712 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7X95 The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab709 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7X96 The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab847 Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7X9E Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
809–833（25 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；289 K；0.1M sodium citrate pH 4.5, 20% PEG 4000
|
Resolution 2.60 Å R-free 0.243 |
| 7X9E Crystal structure of the 76E1 Fab in complex with a SARS-CoV-2 spike peptide Deposited 2022-03-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
809–833（25 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.5；289 K；0.1M sodium citrate pH 4.5, 20% PEG 4000
|
Resolution 2.60 Å R-free 0.243 |
| 7XA7 Crystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2 Deposited 2022-03-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
319–541（223 aa）
Fragment：Receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium acetate trihydrate, 0.1 M sodium citrate pH 5.5, 5 % (w/v) PEG 4000
|
Resolution 3.31 Å R-free 0.254 |
| 7XA7 Crystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2 Deposited 2022-03-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：Receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium acetate trihydrate, 0.1 M sodium citrate pH 5.5, 5 % (w/v) PEG 4000
|
Resolution 3.31 Å R-free 0.254 |
| 7XA7 Crystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2 Deposited 2022-03-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
319–541（223 aa）
Fragment：Receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium acetate trihydrate, 0.1 M sodium citrate pH 5.5, 5 % (w/v) PEG 4000
|
Resolution 3.31 Å R-free 0.254 |
| 7XA7 Crystal structure of SARS-CoV-2 receptor-binding domain in complex with intermediate horseshoe bat ACE2 Deposited 2022-03-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
319–541（223 aa）
Fragment：Receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium acetate trihydrate, 0.1 M sodium citrate pH 5.5, 5 % (w/v) PEG 4000
|
Resolution 3.31 Å R-free 0.254 |
| 7XAZ Crystal structure of Omicron BA.1.1 RBD complexed with hACE2 Deposited 2022-03-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：Omicron RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2 M Potassium thiocyanate 20 % w/v PEG 3350
|
Resolution 3.00 Å R-free 0.230 |
| 7XAZ Crystal structure of Omicron BA.1.1 RBD complexed with hACE2 Deposited 2022-03-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–527（195 aa）
Fragment：Omicron RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2 M Potassium thiocyanate 20 % w/v PEG 3350
|
Resolution 3.00 Å R-free 0.230 |
| 7XB0 Crystal structure of Omicron BA.2 RBD complexed with hACE2 Deposited 2022-03-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：Omicron BA.2 RBD
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；0.1 M ammonium acetate, 0.1 M Bis-Tris
|
Resolution 2.90 Å R-free 0.255 |
| 7XB1 Crystal structure of Omicron BA.3 RBD complexed with hACE2 Deposited 2022-03-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：BA.3 RBD
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M Imidazole pH7.0, 12% w/v Polyethylene glycol 20000
|
Resolution 2.70 Å R-free 0.248 |
| 7XBY The crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in complex with equine ACE2 Deposited 2022-03-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | ZN ZINC ION × 1 BR BROMIDE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium bromide, 0.1M Bis-Tris propane 8.5, 20 % (w/v) PEG 3350
|
Resolution 2.85 Å R-free 0.263 |
| 7XCH Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with human ACE2 ectodomain (two-RBD-up state) Deposited 2022-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7XCI Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with human ACE2 ectodomain (local refinement) Deposited 2022-03-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：UNP residues 333-527
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7XCK Cryo-EM structure of SARS-CoV-2 Omicron RBD in complex with S309 fab (local refinement) Deposited 2022-03-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain M
322–590（269 aa）
Fragment：UNP residues 322-590
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7XCO Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with S309 fab Deposited 2022-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 7XCP Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab Deposited 2022-03-24 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
333–527（195 aa）
Fragment：UNP residues 333-527
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.05 Å |
| 7XCZ Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with BA7054 and BA7125 fab (local refinement) Deposited 2022-03-26 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–528（196 aa）
|
Mutation：L435R, T461K | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7XD2 SARS-CoV-2 S ectodomain trimer in complex with neutralizing antibody 10-5B Deposited 2022-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G,R683S,R685S,K986P,V987P Mutation：R682G,R683S,R685S,K986P,V987P Mutation：R682G,R683S,R685S,K986P,V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7XDA Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with BA7208 and BA7125 fab (local refinement) Deposited 2022-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
334–528（195 aa）
|
Mutation：L434R, T460K | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 7XDB Cryo-EM structure of SARS-CoV-2 Omicron Spike protein in complex with BA7208 fab Deposited 2022-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
26–1144（1119 aa）
Chain B
26–1144（1119 aa）
Chain C
26–1144（1119 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.62 Å |
| 7XDK Cryo-EM structure of SARS-CoV-2 Delta Spike protein in complex with BA7054 and BA7125 fab Deposited 2022-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
26–1143（1118 aa）
Chain B
26–1143（1118 aa）
Chain C
26–1143（1118 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7XDL Cryo-EM structure of SARS-CoV-2 Delta Spike protein in complex with BA7208 and BA7125 fab Deposited 2022-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
26–1143（1118 aa）
Chain B
26–1143（1118 aa）
Chain C
26–1143（1118 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å |
| 7XEG SARS-CoV-2-Beta-RBD and CB6-092-Fab complex Deposited 2022-03-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；Tris pH 8.0, PEG 2000
|
Resolution 2.69 Å R-free 0.248 |
| 7XEG SARS-CoV-2-Beta-RBD and CB6-092-Fab complex Deposited 2022-03-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；Tris pH 8.0, PEG 2000
|
Resolution 2.69 Å R-free 0.248 |
| 7XEI SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex Deposited 2022-03-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；Ammonium nitrate, PEG 3350
|
Resolution 2.76 Å R-free 0.263 |
| 7XEI SARS-CoV-2-prototyped-RBD and CB6-092-Fab complex Deposited 2022-03-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；Ammonium nitrate, PEG 3350
|
Resolution 2.76 Å R-free 0.263 |
| 7XH8 The structure of ZCB11 Fab against SARS-CoV-2 Omicron Spike Deposited 2022-04-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：deletions, insertions, R682G, R683S, R685S, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.99 Å |
| 7XIC S-ECD (Omicron) in complex with STS165 Deposited 2022-04-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：deletions, insertions, K986P, V987P Mutation：deletions, insertions, K986P, V987P Mutation：deletions, insertions, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7XID S-ECD (Omicron) in complex with PD of ACE2 Deposited 2022-04-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：deletions, insersions, K986P, V987P Mutation：deletions, insersions, K986P, V987P Mutation：deletions, insersions, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7XIK SARS-CoV-2-Omicron-RBD and B38-GWP/P-VK antibody complex Deposited 2022-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；15% v/v 2-Propanol, 0.1M Sodium citrate tribasic dihydrate pH 5.0, 10% Polyethylene glycol 10000
|
Resolution 2.89 Å R-free 0.263 |
| 7XIL SARS-CoV-2-Beta-RBD and B38-GWP/P-VK antibody complex Deposited 2022-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Imidazole malate, 15% W/V PEG 4000
|
Resolution 2.91 Å R-free 0.256 |
| 7XIW SARS-CoV-2 Omicron BA.2 variant spike (state 1) Deposited 2022-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain D
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 7XIX SARS-CoV-2 Omicron BA.2 variant spike (state 2) Deposited 2022-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 7XIY SARS-CoV-2 Omicron BA.3 variant spike Deposited 2022-04-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 7XIZ SARS-CoV-2 Omicron BA.3 variant spike (local) Deposited 2022-04-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
323–589（267 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.74 Å |
| 7XJ6 SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 1 conformation Deposited 2022-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 7XJ8 SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab in the class 2 conformation Deposited 2022-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7XJ9 Local refinement of the SARS-CoV-2 BA.1 Spike trimer in complex with 55A8 Fab and 58G6 Fab Deposited 2022-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain B
334–527（194 aa）
Fragment：UNP residues 334-527
Chain C
334–527（194 aa）
Fragment：UNP residues 334-527
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 7XMX Cryo-EM structure of SARS-CoV-2 spike glycoprotein in complex with three F61 Fab Deposited 2022-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 7XMZ Cryo-EM structure of SARS-CoV-2 spike glycoprotein in complex with three D2 Fab Deposited 2022-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.25 Å |
| 7XNQ SARS-CoV-2 Omicron BA.4 variant spike Deposited 2022-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7XNR SARS-CoV-2 Omicron BA.2.13 variant spike Deposited 2022-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 7XNS SARS-CoV-2 Omicron BA.2.12.1 variant spike Deposited 2022-04-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 7XO4 SARS-CoV-2 Omicron BA.1 Variant Spike Trimer with two mouse ACE2 Bound Deposited 2022-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.24 Å |
| 7XO5 SARS-CoV-2 Omicron BA.1 Variant Spike Trimer with one mouse ACE2 Bound Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.13 Å |
| 7XO6 SARS-CoV-2 Omicron BA.1 Variant RBD with mouse ACE2 Bound Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7XO7 SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with two human ACE2 Bound Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 CL CHLORIDE ION × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 7XO8 SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three human ACE2 Bound Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 CL CHLORIDE ION × 3 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.48 Å |
| 7XO9 SARS-CoV-2 Omicron BA.2 Variant RBD complexed with human ACE2 Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1273（1273 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | CL CHLORIDE ION × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7XOA SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with one mouse ACE2 Bound Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7XOB SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with two mouse ACE2 Bound Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7XOC SARS-CoV-2 Omicron BA.2 Variant RBD complexed with mouse ACE2 Deposited 2022-05-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1273（1273 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7XOD SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three JMB2002 Fab Bound Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 7XOE Cryo-EM structure of S glycoprotein encoded by the Covid-19 mRNA vaccine candidate RQ3013 (Prefusion state) Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1255（1255 aa）
Chain B
1–1255（1255 aa）
Chain C
1–1255（1255 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7XOG Cryo-EM structure of S glycoprotein encoded by the Covid-19 mRNA vaccine candidate RQ3013 (Postfusion state) Deposited 2022-05-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1255（1255 aa）
Chain B
1–1255（1255 aa）
Chain C
1–1255（1255 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MAN alpha-D-mannopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7XQS The structure of FLA-K*00701/KP-CoV-9 Deposited 2022-05-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
815–823（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291.15 K；0.1M Sodium chloride, 0.1M HEPES PH 7, 25% (W/V) SOKALAN PA 25 CL
|
Resolution 2.69 Å R-free 0.292 |
| 7XRP Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2 (localized refinement) Deposited 2022-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
27–309（283 aa）
Fragment：NTD
Chain F
330–521（192 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.88 Å |
| 7XS8 Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-1H1 Fab Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；2% v/v Tacsimate pH 5.0, 0.1M Sodium citrate tribasic dihydrate pH 5.4, 13% w/v Polyethylene glycol 3350
|
Resolution 2.80 Å R-free 0.267 |
| 7XSA Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P2S-2E9 Fab Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–527（195 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；15% v/v 2-Propanol, 0.1M Sodium citrate tribasic dihydrate pH 4.8, 11% w/v Polyethylene glycol 10000
|
Resolution 2.20 Å R-free 0.283 |
| 7XSA Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P2S-2E9 Fab Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
333–527（195 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；15% v/v 2-Propanol, 0.1M Sodium citrate tribasic dihydrate pH 4.8, 11% w/v Polyethylene glycol 10000
|
Resolution 2.20 Å R-free 0.283 |
| 7XSB Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.05M Citric acid pH 4.4, 0.05M BIS-TRIS propane, 16% w/v Polyethylene glycol 3350
|
Resolution 3.20 Å R-free 0.324 |
| 7XSB Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.05M Citric acid pH 4.4, 0.05M BIS-TRIS propane, 16% w/v Polyethylene glycol 3350
|
Resolution 3.20 Å R-free 0.324 |
| 7XSB Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.05M Citric acid pH 4.4, 0.05M BIS-TRIS propane, 16% w/v Polyethylene glycol 3350
|
Resolution 3.20 Å R-free 0.324 |
| 7XSB Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.05M Citric acid pH 4.4, 0.05M BIS-TRIS propane, 16% w/v Polyethylene glycol 3350
|
Resolution 3.20 Å R-free 0.324 |
| 7XSC Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-2B10 Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M Magnesium sulfate heptahydrate, 17% w/v Polyethylene glycol 3350
|
Resolution 2.88 Å R-free 0.250 |
| 7XSC Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-2B10 Deposited 2022-05-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
319–529（211 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M Magnesium sulfate heptahydrate, 17% w/v Polyethylene glycol 3350
|
Resolution 2.88 Å R-free 0.250 |
| 7XST Cryo-EM structure of SARS-CoV-2 Omicron spike glycoprotein in complex with three F61 Fab and three D2 Fab Deposited 2022-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 7XTZ Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-1 Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1141（1128 aa）
Chain B
14–1141（1128 aa）
Chain C
14–1141（1128 aa）
|
Mutation：D427C, V987C Mutation：D427C, V987C Mutation：D427C, V987C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 BLA BILIVERDINE IX ALPHA × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7XU0 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-211 Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1141（1128 aa）
Chain B
14–1141（1128 aa）
Chain C
14–1141（1128 aa）
|
Mutation：D427C, V987C Mutation：D427C, V987C Mutation：D427C, V987C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 EIC LINOLEIC ACID × 3 BLA BILIVERDINE IX ALPHA × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7XU1 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-122 Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：D427C, V987C Mutation：D427C, V987C Mutation：D427C, V987C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 BLA BILIVERDINE IX ALPHA × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7XU2 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-2 Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1140（1127 aa）
Chain B
14–1140（1127 aa）
Chain C
14–1140（1127 aa）
|
Mutation：D427C, V987C Mutation：D427C, V987C Mutation：D427C, V987C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 BLA BILIVERDINE IX ALPHA × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7XU3 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1140（1127 aa）
Chain B
14–1140（1127 aa）
Chain C
14–1140（1127 aa）
|
Mutation：D427C, V987C Mutation：D427C, V987C Mutation：D427C, V987C | BLA BILIVERDINE IX ALPHA × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7XU4 Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Locked-2 Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1140（1127 aa）
Chain B
14–1140（1127 aa）
Chain C
14–1140（1127 aa）
|
Mutation：D427C, D614G, V987C Mutation：D427C, D614G, V987C Mutation：D427C, D614G, V987C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 BLA BILIVERDINE IX ALPHA × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7XU5 Structure of SARS-CoV-2 D614G Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), Closed Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1140（1127 aa）
Chain B
14–1140（1127 aa）
Chain C
14–1140（1127 aa）
|
Mutation：D614G, D427C, V987C Mutation：D614G, D427C, V987C Mutation：D614G, D427C, V987C | BLA BILIVERDINE IX ALPHA × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7XU6 Structure of SARS-CoV-2 Spike Protein with Engineered x3 Disulfide (x3(D427C, V987C) and single Arg S1/S2 cleavage site), incubated in Low pH after 40-Day Storage in PBS, Locked-2 Conformation Deposited 2022-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1140（1127 aa）
Chain B
14–1140（1127 aa）
Chain C
14–1140（1127 aa）
|
Mutation：D427C, V987C Mutation：D427C, V987C Mutation：D427C, V987C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 BLA BILIVERDINE IX ALPHA × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 7XWA Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2 Deposited 2022-05-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
322–536（215 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1M MES pH6.5, 11-13% PEG6000, 5% MPD
|
Resolution 3.36 Å R-free 0.287 |
| 7XWA Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2 Deposited 2022-05-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
322–536（215 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1M MES pH6.5, 11-13% PEG6000, 5% MPD
|
Resolution 3.36 Å R-free 0.287 |
| 7XXL RBD in complex with Fab14 Deposited 2022-05-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
331–532（202 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；PBS pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.30 Å |
| 7XY3 Cryo-EM structure of SARS-CoV-2 spike in complex with VHH14 Deposited 2022-05-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1145（1132 aa）
Chain B
14–1145（1132 aa）
Chain C
14–1145（1132 aa）
|
Mutation：R682G, R683G, R685S, K986P and V987P Mutation：R682G, R683G, R685S, K986P and V987P Mutation：R682G, R683G, R685S, K986P and V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.60 Å |
| 7XY4 Cryo-EM structure of SARS-CoV-2 spike in complex with VHH21 Deposited 2022-05-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1145（1132 aa）
Chain B
14–1145（1132 aa）
Chain C
14–1145（1132 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 40 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7Y0C Crystal structure of BD55-1403 and SARS-CoV-2 Omicron RBD Deposited 2022-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
330–528（199 aa）
Fragment：Omicron RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION, RECRYSTALLIZATION；pH 5；291.15 K；PEG3350, Sodium citrate tribasic dihydrate
|
Resolution 2.94 Å R-free 0.278 |
| 7Y0C Crystal structure of BD55-1403 and SARS-CoV-2 Omicron RBD Deposited 2022-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–528（199 aa）
Fragment：Omicron RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION, RECRYSTALLIZATION；pH 5；291.15 K；PEG3350, Sodium citrate tribasic dihydrate
|
Resolution 2.94 Å R-free 0.278 |
| 7Y0N SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody Deposited 2022-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1147（1147 aa）
Chain B
1–1147（1147 aa）
Chain D
1–1147（1147 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7Y0O Interface of SARS-CoV-2 WT Spike in complex with R15 Fab and P14 Nanobody Deposited 2022-06-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
334–527（194 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7Y0V The co-crystal structure of BA.1-RBD with Fab-5549 Deposited 2022-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
325–541（217 aa）
Fragment：BA.1-RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.25；291 K；0.1 M HEPES sodium pH 7.25, 10% v/v 2-Propanol, 18% w/v Polyethylene glycol 4,000
|
Resolution 2.48 Å R-free 0.268 |
| 7Y0W Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 RBD complex Deposited 2022-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
335–527（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen OTHER
|
Resolution 3.42 Å |
| 7Y1Y S-ECD (Omicron BA.2) in complex with PD of ACE2 Deposited 2022-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：P986K,P987V Mutation：P986K,P987V Mutation：P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7Y1Z S-ECD (Omicron BA.3) in complex with three PD of ACE2 Deposited 2022-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：P986K,P987V Mutation：P986K,P987V Mutation：P986K,P987V | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7Y20 S-ECD (Omicron BA.3) in complex with two PD of ACE2 Deposited 2022-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7Y21 S-ECD (Omicron BA.5) in complex with PD of ACE2 Deposited 2022-06-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7Y3O Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody BIOLS56 Deposited 2022-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.2 M Imidazole malate, pH 7.0, 20% w/v PEG 4000
|
Resolution 2.10 Å R-free 0.229 |
| 7Y42 Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic acid Deposited 2022-06-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain D
27–1147（1121 aa）
|
Mutation：C66F, K986P, V987P Mutation：C66F, K986P, V987P Mutation：C66F, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 REA RETINOIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 7Y6D Cryo-EM structure of SARS-CoV-2 Delta variant spike proteins on intact virions: 3 Closed RBD Deposited 2022-06-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 4.39 Å |
| 7Y6K Cryo-EM structure of SARS-CoV-2 receptor binding domain in complex with K202.B bispecific antibody Deposited 2022-06-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: tetrameric |
Chain B
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 7Y6L The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab816 Deposited 2022-06-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7Y6N The SARS-CoV-2 receptor binding domain bound with the Fab fragment of a human neutralizing antibody Ab803 Deposited 2022-06-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7Y71 SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 Deposited 2022-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
16–1213（1198 aa）
Chain B
16–1213（1198 aa）
Chain C
16–1213（1198 aa）
|
Mutation：R683A, R685A, F817P, A892P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 7Y72 SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 (focused refinement on Fab-RBD interface) Deposited 2022-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
16–1213（1198 aa）
Chain C
16–1213（1198 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.03 Å |
| 7Y75 SIT1-ACE2-BA.2 RBD Deposited 2022-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
319–541（223 aa）
Fragment：BA.2 RBD
Chain F
319–541（223 aa）
Fragment：BA.2 RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE × 6 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7Y76 SIT1-ACE2-BA.5 RBD Deposited 2022-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
319–541（223 aa）
Fragment：BA.4 RBD
Chain F
319–541（223 aa）
Fragment：BA.4 RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE × 6 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7Y7J SARS-CoV-2 S trimer in complex with 1F Fab Deposited 2022-06-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：YES Mutation：YES Mutation：YES | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7Y7K SARS-CoV-2 RBD in complex with 1F Fab Deposited 2022-06-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
336–514（179 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 7Y8J 3D1 in complex with 6-mer HR1 peptide from SARS-CoV-2 Deposited 2022-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
950–956（7 aa）
Fragment：HR1 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M HEPES pH7.5, 25% PEG8000
|
Resolution 1.03 Å R-free 0.145 |
| 7Y9N an engineered 5-helix bundle derived from SARS-CoV-2 S2 in complex with HR2P Deposited 2022-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
918–967（50 aa）
Chain A
1167–1203（37 aa）
Chain B
1168–1203（36 aa）
Fragment：HR2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Citric acid (pH 3.5), 14% w/v Polyethylene glycol 1000
|
Resolution 1.89 Å R-free 0.212 |
| 7Y9S Cryo-EM structure of apo SARS-CoV-2 Omicron spike protein (S-2P-GSAS) Deposited 2022-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–1208（1194 aa）
Chain B
15–1208（1194 aa）
Chain C
15–1208（1194 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 7Y9Z Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with human ACE2 ectodomain (one-RBD-up state) Deposited 2022-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 7YA0 Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (S-6P-RRAR) Deposited 2022-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Mutation：F817P, A892P, A899P,A942P,K986P, V987P Mutation：F817P, A892P, A899P,A942P,K986P, V987P Mutation：F817P, A892P, A899P,A942P,K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7YA1 Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (local refinement) Deposited 2022-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 7YAD Cryo-EM structure of S309-RBD-RBD-S309 in the S309-bound Omicron spike protein (local refinement) Deposited 2022-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
330–529（200 aa）
Chain M
330–529（200 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 7YBH SARS-CoV-2 lambda variant spike Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
|
Resolution 3.50 Å |
| 7YBI SARS-CoV-2 Mu variant spike (open state) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7YBJ SARS-CoV-2 Mu variant spike(close state) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.73 Å |
| 7YBK SARS-CoV-2 B.1.620 variant spike (open state) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
|
Resolution 3.90 Å |
| 7YBL SARS-CoV-2 B.1.620 variant spike (close state) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7YBM SARS-CoV-2 C.1.2 variant spike (Close state) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 7YBN SARS-CoV-2 C.1.2 variant spike (Open state) Deposited 2022-06-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：A892P, A899P, A942P Mutation：A892P, A899P, A942P Mutation：A892P, A899P, A942P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
|
Resolution 3.82 Å |
| 7YC5 Cryo-EM structure of SARS-CoV-2 spike in complex with K202.B bispecific antibody Deposited 2022-06-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7YCK Crystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；293.15 K；0.2M Ammonium sulfate; 0.05 M Magnesium sulfate heptahydrate, 0.1M BICINE pH 9.0, 2.5% w/v PEG 3350, 2.5%w/v PEG 4000, 2.5% w/v PEG 2000, 2.5% w/v PEG 5000 MME
|
Resolution 2.60 Å R-free 0.264 |
| 7YCK Crystal structure of SARS-CoV-2 Spike RBD in complex with FP-12A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9；293.15 K；0.2M Ammonium sulfate; 0.05 M Magnesium sulfate heptahydrate, 0.1M BICINE pH 9.0, 2.5% w/v PEG 3350, 2.5%w/v PEG 4000, 2.5% w/v PEG 2000, 2.5% w/v PEG 5000 MME
|
Resolution 2.60 Å R-free 0.264 |
| 7YCL Crystal structure of SARS-CoV-2 Spike RBD in complex with IS-9A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；2% v/v 1,4-Dioxane, 0.1M Tris pH 8.0, 15% w/v Polyethylene glycol 3350
|
Resolution 2.13 Å R-free 0.217 |
| 7YCL Crystal structure of SARS-CoV-2 Spike RBD in complex with IS-9A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；2% v/v 1,4-Dioxane, 0.1M Tris pH 8.0, 15% w/v Polyethylene glycol 3350
|
Resolution 2.13 Å R-free 0.217 |
| 7YCN Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2M Ammonium citrate tribasic pH 7.0, 0.1M Imidazole pH 7.0, 20% w/v Polyethylene glycol monomethyl ether
|
Resolution 2.85 Å R-free 0.250 |
| 7YCN Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2M Ammonium citrate tribasic pH 7.0, 0.1M Imidazole pH 7.0, 20% w/v Polyethylene glycol monomethyl ether
|
Resolution 2.85 Å R-free 0.250 |
| 7YCN Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2M Ammonium citrate tribasic pH 7.0, 0.1M Imidazole pH 7.0, 20% w/v Polyethylene glycol monomethyl ether
|
Resolution 2.85 Å R-free 0.250 |
| 7YCN Crystal structure of SARS-CoV-2 Spike RBD in complex with IY-2A Fab Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
333–527（195 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.2M Ammonium citrate tribasic pH 7.0, 0.1M Imidazole pH 7.0, 20% w/v Polyethylene glycol monomethyl ether
|
Resolution 2.85 Å R-free 0.250 |
| 7YCO Crystal structure of SARS-CoV-2 Receptor Binding Domain bound to A6 repebody Deposited 2022-07-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–530（198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium citrate tribasic dihydrate, 20 % (w/v) PEG 3350
|
Resolution 1.96 Å R-free 0.259 |
| 7YCY SARS-CoV-2 Omicron 1-RBD up Spike trimer complexed with three XG005 molecules Deposited 2022-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.74 Å |
| 7YCZ SARS-CoV-2 Omicron 2-RBD up Spike trimer complexed with three XG005 molecules Deposited 2022-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.24 Å |
| 7YD0 SARS-CoV-2 Omicron 1-RBD up spike trimer complexed with two XG005 Fab Deposited 2022-07-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 7YD1 Local refinement of SARS-CoV-2 Omicron S trimer complexed with XG005 Deposited 2022-07-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
331–528（198 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.99 Å |
| 7YDI SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2, focused refinement of RBD region Deposited 2022-07-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
334–526（193 aa）
Fragment：Spike protomer RBD domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.98 Å |
| 7YDY SARS-CoV-2 Spike (6P) in complex with 1 R1-32 Fab Deposited 2022-07-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.75 Å |
| 7YE5 SARS-CoV-2 Spike (6P) in complex with 2 R1-32 Fabs Deposited 2022-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.75 Å |
| 7YE9 SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs Deposited 2022-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.17 Å |
| 7YEG SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2 Deposited 2022-07-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R682S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 ZN ZINC ION × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.73 Å |
| 7YH6 Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-8 Deposited 2022-07-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；octyl-maltoside, fluorinated solution was added to PBS solution to a final concentration of 0.01%
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.40 Å |
| 7YH7 SARS-CoV-2 spike in complex with neutralizing antibody NIV-8 (state 2) Deposited 2022-07-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：R682G, R683S, R685G, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685G, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685G, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.30 Å |
| 7YHW Cryo-EM structure of SARS-CoV-2 Omicron BA.2.12.1 RBD in complex with human ACE2 (local refinement) Deposited 2022-07-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
| 7YJ3 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with human ACE2 (local refinement) Deposited 2022-07-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：RBD
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 7YKJ Omicron RBDs bound with P3E6 Fab (one up and one down) Deposited 2022-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7YOW Crystal structure of SARS-CoV-2 omicron variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab Deposited 2022-08-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
321–536（216 aa）
|
Not recorded | SO4 SULFATE ION × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.5 M ammonium sulfate, 19.5% PEG 3350, 1 mM EDTA, 10% golycerol, 0.1 M Bis-Tris pH 5.5
|
Resolution 3.30 Å R-free 0.254 |
| 7YOW Crystal structure of SARS-CoV-2 omicron variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab Deposited 2022-08-02 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
321–536（216 aa）
|
Not recorded | SO4 SULFATE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.5 M ammonium sulfate, 19.5% PEG 3350, 1 mM EDTA, 10% golycerol, 0.1 M Bis-Tris pH 5.5
|
Resolution 3.30 Å R-free 0.254 |
| 7YQT SARS-CoV-2 BA.2.75 S Trimer (1 RBD Up) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 7YQU SARS-CoV-2 BA.2.75 S Trimer (3 RBD Down) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.19 Å |
| 7YQV pH 5.5 SARS-CoV-2 BA.2.75 S Trimer (1 RBD Up) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.58 Å |
| 7YQW SARS-CoV-2 BA.2.75 S Trimer (3 RBD Down) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.51 Å |
| 7YQX SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state1) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 7YQY SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state2) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.74 Å |
| 7YQZ SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (state3) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
| 7YR0 SARS-CoV-2 BA.2.75 S Trimer in complex with S309 (interface) Deposited 2022-08-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–527（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.98 Å |
| 7YR1 SARS-CoV-2 BA.2.75 S Trimer in complex with XG2v024 Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 7YR2 SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state1) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–1273（1273 aa）
Chain D
1–1273（1273 aa）
Chain E
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942A, K986P, V987P | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 49 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7YR3 SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state2) Deposited 2022-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
Chain F
1–1273（1273 aa）
|
Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683A, R685A, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 53 ZN ZINC ION × 2 CL CHLORIDE ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 7YR4 SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(interface) Deposited 2022-08-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–528（195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.12 Å |
| 7YTN Crystal structure of SARS-CoV-2 Alpha RBD in complex with the D27LEY neutralizing antibody Fab fragment Deposited 2022-08-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；200 mM ammonium citrate tribasic (pH 7.0), 20% (v/v) polyethyleneglycol 3350
|
Resolution 3.51 Å R-free 0.274 |
| 7YUE Epitope-directed anti-SARS CoV 2 scFv engineered against the key spike protein region. Deposited 2022-08-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
815–826（12 aa）
Fragment：SARS CoV 2 epitope
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；0.2 M sodium thiocyanate at pH 5.9
20% PEG 1000
|
Resolution 2.35 Å R-free 0.232 |
| 7YV8 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with golden hamster ACE2 (local refinement) Deposited 2022-08-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
332–528（197 aa）
Fragment：RBD
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 7YVE Omicron BA.4/5 SARS-CoV-2 S in complex with TH027 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7YVF Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH027 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7YVG Omicron BA.4/5 SARS-CoV-2 S in complex with TH132 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7YVH Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH132 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7YVI Omicron BA.4/5 SARS-CoV-2 S in complex with TH236 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7YVJ Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH236 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7YVK Omicron BA.4/5 SARS-CoV-2 S in complex with TH272 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7YVL Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH272 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7YVM Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH272 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7YVN Omicron BA.4/5 SARS-CoV-2 S in complex with TH281 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7YVO Omicron BA.4/5 SARS-CoV-2 S in complex with TH027/132 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 7YVP Omicron BA.4/5 SARS-CoV-2 S in complex with TH272/281 Fab Deposited 2022-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P Mutation：K986P, V987P Mutation：K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7YVU Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement) Deposited 2022-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 7Z0X THSC20.HVTR26 Fab bound to SARS-CoV-2 Receptor Binding Domain Deposited 2022-02-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
331–527（197 aa）
|
Not recorded | EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；293.15 K；15% (w/v) PEG 20,000, 100 mM HEPES / Sodium hydroxide pH 7.0
|
Resolution 1.80 Å R-free 0.188 |
| 7Z0Y THSC20.HVTR04 Fab bound to SARS-CoV-2 Receptor Binding Domain Deposited 2022-02-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
331–527（197 aa）
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293 K；1.5M ammonium sulfate, 12%(v/v) isopropanol, 0.1M imidazole HCl pH 6.5
|
Resolution 2.95 Å R-free 0.241 |
| 7Z1A Nanobody H11 and F2 bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BICINE pH 8.5, 20% w/v Polyethylene glycol 10,000
|
Resolution 2.59 Å R-free 0.241 |
| 7Z1A Nanobody H11 and F2 bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BICINE pH 8.5, 20% w/v Polyethylene glycol 10,000
|
Resolution 2.59 Å R-free 0.241 |
| 7Z1B Nanobody H11-A10 and F2 bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate, pH 5.5, 20 % Peg 3000
|
Resolution 2.30 Å R-free 0.243 |
| 7Z1B Nanobody H11-A10 and F2 bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate, pH 5.5, 20 % Peg 3000
|
Resolution 2.30 Å R-free 0.243 |
| 7Z1C Nanobody H11-B5 and H11-F2 bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4,000
|
Resolution 1.90 Å R-free 0.199 |
| 7Z1C Nanobody H11-B5 and H11-F2 bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25% w/v Polyethylene glycol 4,000
|
Resolution 1.90 Å R-free 0.199 |
| 7Z1D Nanobody H11-H6 bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain EEE
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES, pH 7.5 and 20% w/v PEG 8000
|
Resolution 1.55 Å R-free 0.186 |
| 7Z1E Nanobody H11-H4 Q98R H100E bound to RBD Deposited 2022-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain EEE
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 NO3 NITRATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium nitrate, 20 % Peg 3350
|
Resolution 1.59 Å R-free 0.202 |
| 7Z3Z Locked Wuhan SARS-CoV2 Prefusion Spike ectodomain with lipid bound Deposited 2022-03-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 STE STEARIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7Z6V CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11 nanobody complex Deposited 2022-03-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 120 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 82% relative humidity and ambient temperature.
|
Resolution 3.10 Å |
| 7Z7X CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H6 nanobody complex Deposited 2022-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 120 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) or for 60-80 s, 12 mA (easiGlow, Pelco) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 79-81% relative humidity and ambient temperature.
|
Resolution 3.30 Å |
| 7Z85 CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-B5 nanobody complex Deposited 2022-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 190 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 83% relative humidity and ambient temperature.
|
Resolution 3.10 Å |
| 7Z86 CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 1Up2Down conformation Deposited 2022-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7Z8O Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide Deposited 2022-03-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–527（195 aa）
|
Not recorded | GOL GLYCEROL × 3 KZ0 2,4,6-tris(chloromethyl)-1,3,5-triazine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；22 %v/v PEGSB,
0.1 M Na Phos Cit 5.5 pH
|
Resolution 0.96 Å R-free 0.169 |
| 7Z9Q CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex Deposited 2022-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；SPT Labtech prototype 300 mesh 1.2/2.0 nanowire grids with a highly reproduceable rectangular bar cross-section were used. The grids were glow-discharged on low for 260 s (Plasma Cleaner PDC-002-CE, Harrick Plasma) to activate the nanowires. Approximately 6 nL of the complex were applied to the grids using a Chameleon EP system (SPT Labtech) at 80% relative humidity and ambient temperature.
|
Resolution 3.60 Å |
| 7Z9R CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-H4 Q98R H100E nanobody complex in 2Up1Down conformation Deposited 2022-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7ZBU CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60 Deposited 2022-03-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 3Q9 3-[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-2-[[5-[(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；0.1% n-octyl glucoside in 150 mM NaCl, 20 mM Tris-HCl, pH8.0
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 3 to 4 sec before plunging
|
Resolution 4.31 Å |
| 7ZCE SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76 Deposited 2022-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7ZCF SARS-CoV-2 Spike RBD in complex with the single chain fragment scFv76 (Focused Refinement) Deposited 2022-03-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7ZDQ Cryo-EM structure of Human ACE2 bound to a high-affinity SARS CoV-2 mutant Deposited 2022-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Mutation：Q498H, S477N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Blot for 3 seconds. Wait time of 30 seconds for graphene oxide grids and 0 seconds for holey grids.
|
Resolution 3.20 Å |
| 7ZF3 SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 4 IPA ISOPROPYL ALCOHOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate pH 5.0, 30% (v/v) Jeffamine ED-2001 pH 7.0
|
Resolution 3.15 Å R-free 0.266 |
| 7ZF4 SARS-CoV-2 Omicron RBD in complex with Omi-9 Fab and nanobody F2 Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium acetate trihydrate pH 4.5 and 30% (w/v) PEG 1500
|
Resolution 4.18 Å R-free 0.385 |
| 7ZF5 SARS-CoV-2 Omicron RBD in complex with Omi-12 and Beta-54 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 18% (w/v) PEG 20000
|
Resolution 5.32 Å R-free 0.256 |
| 7ZF5 SARS-CoV-2 Omicron RBD in complex with Omi-12 and Beta-54 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.0, 18% (w/v) PEG 20000
|
Resolution 5.32 Å R-free 0.256 |
| 7ZF7 SARS-CoV-2 Omicron BA.2 RBD in complex with ACE2 Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.09 M MES monohydrate pH 6.0, 18% (w/v) PEG monomethyl ether 2000
|
Resolution 3.46 Å R-free 0.269 |
| 7ZF8 SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.5, 18% (w/v) PEG 3350
|
Resolution 2.95 Å R-free 0.258 |
| 7ZF9 SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab (P21) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium acetate trihydrate pH 4.5 and 30% (w/v) PEG 1500
|
Resolution 3.25 Å R-free 0.265 |
| 7ZF9 SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab (P21) Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium acetate trihydrate pH 4.5 and 30% (w/v) PEG 1500
|
Resolution 3.25 Å R-free 0.265 |
| 7ZFA SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES pH 7.0, 15 % w/v PEG 4000
|
Resolution 4.24 Å R-free 0.272 |
| 7ZFA SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES pH 7.0, 15 % w/v PEG 4000
|
Resolution 4.24 Å R-free 0.272 |
| 7ZFA SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES pH 7.0, 15 % w/v PEG 4000
|
Resolution 4.24 Å R-free 0.272 |
| 7ZFA SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium HEPES pH 7.0, 15 % w/v PEG 4000
|
Resolution 4.24 Å R-free 0.272 |
| 7ZFB SARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20 % w/v PEG 8000
|
Resolution 3.08 Å R-free 0.308 |
| 7ZFB SARS-CoV-2 Omicron RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain F
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.1 M MES pH 6.5, 20 % w/v PEG 8000
|
Resolution 3.08 Å R-free 0.308 |
| 7ZFC SARS-CoV-2 Beta RBD in complex with nanobody C1, Omi-18 and Omi-31 Fabs Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.04 M Potassium phosphate monobasic, 16% w/v PEG 8000
|
Resolution 3.24 Å R-free 0.299 |
| 7ZFD SARS-CoV-2 Omicron RBD in complex with Omi-25 Fab Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
330–532（203 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Proplex 1-31: 3.0 M Sodium formate, 0.1 M Tris pH 7.5
|
Resolution 3.39 Å R-free 0.338 |
| 7ZFD SARS-CoV-2 Omicron RBD in complex with Omi-25 Fab Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
330–532（203 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Proplex 1-31: 3.0 M Sodium formate, 0.1 M Tris pH 7.5
|
Resolution 3.39 Å R-free 0.338 |
| 7ZFE SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% w/v Polyethylene glycol 6,000
|
Resolution 3.25 Å R-free 0.293 |
| 7ZFE SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% w/v Polyethylene glycol 6,000
|
Resolution 3.25 Å R-free 0.293 |
| 7ZFE SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% w/v Polyethylene glycol 6,000
|
Resolution 3.25 Å R-free 0.293 |
| 7ZFE SARS-CoV-2 Omicron RBD in complex with Omi-32 Fab and nanobody C1 Deposited 2022-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% w/v Polyethylene glycol 6,000
|
Resolution 3.25 Å R-free 0.293 |
| 7ZJL Delta SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue. Deposited 2022-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
15–1146（1132 aa）
Chain B
15–1146（1132 aa）
Chain C
15–1146（1132 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 7ZR2 Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2 Deposited 2022-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
915–988（74 aa）
Chain B
1164–1202（39 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；0.1M sodium HEPES, 20% (w/v) PEG4000, 10% (v/v) isopropanol
|
Resolution 1.45 Å R-free 0.209 |
| 7ZR7 OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN Deposited 2022-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7ZR8 OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE RBD (local refinement) Deposited 2022-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 7ZR9 OMI-2 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN Deposited 2022-05-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7ZRC OMI-38 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE Deposited 2022-05-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7ZRV cryo-EM structure of omicron spike in complex with de novo designed binder, full map Deposited 2022-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 7ZSD cryo-EM structure of omicron spike in complex with de novo designed binder, local Deposited 2022-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain M
332–527（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 7ZSS cryo-EM structure of D614 spike in complex with de novo designed binder Deposited 2022-05-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1146（1146 aa）
Chain B
1–1146（1146 aa）
Chain C
1–1146（1146 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.63 Å |
| 7ZXU SARS-CoV-2 Omicron BA.4/5 RBD in complex with Beta-27 Fab and C1 nanobody Deposited 2022-05-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 10 IPA ISOPROPYL ALCOHOL × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；4% (v/v) 2-propanol, 0.1M BIS-Tris propane, pH9.0, 20% (w/v) PEG monomethyl ether 5000
|
Resolution 1.89 Å R-free 0.209 |
| 8A94 SARS CoV2 Spike in the 2-up state in complex with Fab47. Deposited 2022-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 43 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 8A95 SARS Cov2 Spike RBD in complex with Fab47 Deposited 2022-06-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8A96 SARS Cov2 Spike RBD in complex with Fab47 Deposited 2022-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
327–531（205 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8A99 SARS Cov2 Spike in 1-up conformation complex with Fab47 Deposited 2022-06-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 44 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 8AAA Crystal structure of SARS-CoV-2 S RBD in complex with a stapled peptide Deposited 2022-06-30 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–527（195 aa）
|
Not recorded | 29N 1,1',1''-(1,3,5-triazinane-1,3,5-triyl)tripropan-1-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；294 K；22% PEGSM, 2% Glycerol, 0.01M CoCl2, 0.2M MgCl2, 0.1M Bis TRIS
|
Resolution 1.90 Å R-free 0.236 |
| 8AJA Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein Deposited 2022-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.59 Å |
| 8AJL Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein Deposited 2022-07-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8AQS BA.4/5 SARS-CoV-2 Spike bound to human ACE2 (local) Deposited 2022-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.92 Å |
| 8AQT Beta SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8AQU BA.1 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 8AQV BA.2.12.1 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 8AQW BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8ASY SARS-CoV-2 Omicron BA.2.75 RBD in complex with ACE2 Deposited 2022-08-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 12 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 CL CHLORIDE ION × 1 PGE TRIETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1% (w/v) n-Octyl-b-D-glucoside, 0.1 M Sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 3350
|
Resolution 2.85 Å R-free 0.265 |
| 8BBN SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs Deposited 2022-10-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain Y
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5 and 30% (w/v) PEG 1500
|
Resolution 3.58 Å R-free 0.314 |
| 8BBN SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs Deposited 2022-10-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain X
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5 and 30% (w/v) PEG 1500
|
Resolution 3.58 Å R-free 0.314 |
| 8BBN SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs Deposited 2022-10-14 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；10% (v/v) 2-propanol, 0.1 M BICINE, pH 8.5 and 30% (w/v) PEG 1500
|
Resolution 3.58 Å R-free 0.314 |
| 8BCZ SARS-CoV-2 Delta-RBD complexed with Fabs BA.2-36, BA.2-23, EY6A and COVOX-45 Deposited 2022-10-17 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain R
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8BE1 SARS-CoV-2 RBD in complex with a Fab fragment of a neutralising antibody mRBD2 Deposited 2022-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–527（195 aa）
|
Not recorded | SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；281 K；0.1 M Bis Tris Propane pH 6.5 0.2 M Potassium thiocyanate 20 % w/v PEG 3350 10 % v/v Ethylene glycol
|
Resolution 1.98 Å R-free 0.284 |
| 8BE1 SARS-CoV-2 RBD in complex with a Fab fragment of a neutralising antibody mRBD2 Deposited 2022-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–527（195 aa）
|
Not recorded | SO4 SULFATE ION × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；281 K；0.1 M Bis Tris Propane pH 6.5 0.2 M Potassium thiocyanate 20 % w/v PEG 3350 10 % v/v Ethylene glycol
|
Resolution 1.98 Å R-free 0.284 |
| 8BEC Crystal structure of the SARS-CoV-2 S RBD in complex with pT1375 scFV Deposited 2022-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；pT1375-RBD at 15,5 mg/ml using 1.5 M Ammonium sulfate, 15 % w/v glycerol, 100 mM Tris pH 8.5 as reservoir and micro seeds in 18% PEG 3350, 100 mM citrate pH 4, 200 mM Na3Cit stabilization solution
|
Resolution 1.70 Å R-free 0.207 |
| 8BEC Crystal structure of the SARS-CoV-2 S RBD in complex with pT1375 scFV Deposited 2022-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–527（194 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；pT1375-RBD at 15,5 mg/ml using 1.5 M Ammonium sulfate, 15 % w/v glycerol, 100 mM Tris pH 8.5 as reservoir and micro seeds in 18% PEG 3350, 100 mM citrate pH 4, 200 mM Na3Cit stabilization solution
|
Resolution 1.70 Å R-free 0.207 |
| 8BEV Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in complex with nanobody W25 (map 3, focus refinement on RBD, W25 and adjacent NTD) Deposited 2022-10-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE；1s blotting time
|
Resolution 5.92 Å |
| 8BG1 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1511 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；pT1511-RBD at 9.5 mg/ml using 16% PEG 3350, 200 mM sodium malonate, 100 mM Bis-tris propane pH 7.5 as reservoir
|
Resolution 2.88 Å R-free 0.244 |
| 8BG1 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1511 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；pT1511-RBD at 9.5 mg/ml using 16% PEG 3350, 200 mM sodium malonate, 100 mM Bis-tris propane pH 7.5 as reservoir
|
Resolution 2.88 Å R-free 0.244 |
| 8BG1 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1511 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；pT1511-RBD at 9.5 mg/ml using 16% PEG 3350, 200 mM sodium malonate, 100 mM Bis-tris propane pH 7.5 as reservoir
|
Resolution 2.88 Å R-free 0.244 |
| 8BG1 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1511 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；pT1511-RBD at 9.5 mg/ml using 16% PEG 3350, 200 mM sodium malonate, 100 mM Bis-tris propane pH 7.5 as reservoir
|
Resolution 2.88 Å R-free 0.244 |
| 8BG2 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1580 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pT1580-RBD at 9,8 mg/ml using 1.4 M Na-Tartrate, 100 mM Tris pH 8.5 as reservoir
|
Resolution 2.10 Å R-free 0.227 |
| 8BG2 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1580 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pT1580-RBD at 9,8 mg/ml using 1.4 M Na-Tartrate, 100 mM Tris pH 8.5 as reservoir
|
Resolution 2.10 Å R-free 0.227 |
| 8BG3 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1610 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；pT1610-RBD at 10.2 mg/ml using 20% PEG 3350, 100 mM MES pH 6, 200 mM NaF as reservoir
|
Resolution 1.90 Å R-free 0.214 |
| 8BG3 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1610 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；pT1610-RBD at 10.2 mg/ml using 20% PEG 3350, 100 mM MES pH 6, 200 mM NaF as reservoir
|
Resolution 1.90 Å R-free 0.214 |
| 8BG4 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1611 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pT1611-RBD at 18.7 mg/ml using 1.6 M ammonium-sulfate, 2 % PEG 1000, 100 mM HEPES pH 8 as reservoir
|
Resolution 1.60 Å R-free 0.208 |
| 8BG4 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1611 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pT1611-RBD at 18.7 mg/ml using 1.6 M ammonium-sulfate, 2 % PEG 1000, 100 mM HEPES pH 8 as reservoir
|
Resolution 1.60 Å R-free 0.208 |
| 8BG5 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pT1631-RBD at 15.8 mg/ml using 16 % PEG 4000, 100 mM Tris pH 8.5, 200 mM Li2SO4 as reservoir and micro seeds in 18% PEG 3350, 100 mM citrate pH 4, 200 mM Na3Cit stabilization solution
|
Resolution 2.05 Å R-free 0.217 |
| 8BG5 Crystal structure of the SARS-CoV-2 S RBD in complex with pT1631 scFV Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pT1631-RBD at 15.8 mg/ml using 16 % PEG 4000, 100 mM Tris pH 8.5, 200 mM Li2SO4 as reservoir and micro seeds in 18% PEG 3350, 100 mM citrate pH 4, 200 mM Na3Cit stabilization solution
|
Resolution 2.05 Å R-free 0.217 |
| 8BG6 SARS-CoV-2 S protein in complex with pT1644 Fab Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.11 Å |
| 8BG8 SARS-CoV-2 S protein in complex with pT1696 Fab Deposited 2022-10-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.64 Å |
| 8BGG Cryo-EM structure of SARS-CoV-2 spike (Omicron BA.1 variant) in complex with nanobody W25 (map 5, focus refinement on RBD, W25 and adjacent NTD) Deposited 2022-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.04 Å |
| 8BH5 SARS-CoV-2 BA.2.12.1 RBD in complex with Beta-27 Fab and C1 nanobody Deposited 2022-10-29 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–528（196 aa）
|
Not recorded | GOL GLYCEROL × 12 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dehydrate, pH 5.5, 18% w/v Polyethylene glycol 3,350
|
Resolution 2.38 Å R-free 0.233 |
| 8BON Structure of the SARS-CoV-2 spike glycoprotein in complex with the macrocyclic peptide S1B3inL1 Deposited 2022-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8BSE CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD) in complex with 1D1 Fab Deposited 2022-11-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 5 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；18% PEG Smear Broad
0.08 M MgCl2
0.08 M tri-sodium citrate
0.1 M Bis-Tris pH 6.0
|
Resolution 1.90 Å R-free 0.216 |
| 8BSF CRYSTAL STRUCTURE OF SARS-COV-2 RECEPTOR BINDING DOMAIN (RBD-beta variant) in complex with 3D2 Fab Deposited 2022-11-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.04 M potassium dihydrogen phosphate
18 % PEG 8000
20 % glycerol
|
Resolution 2.20 Å R-free 0.229 |
| 8C0Y SARS-CoV2 Omicron BA.1 RBD in complex with CAB-A17 antibody Deposited 2022-12-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.68 Å |
| 8C1V SARS-CoV-2 S-trimer (3 RBDs up) bound to TriSb92, fitted into cryo-EM map Deposited 2022-12-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
26–1149（1124 aa）
Chain B
26–1149（1124 aa）
Chain C
26–1149（1124 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；10 mM Tris pH 8 + 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8C2R SARS-CoV2 Omicron BA.1 spike in complex with CAB-A17 antibody Deposited 2022-12-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
26–1147（1122 aa）
Chain B
26–1147（1122 aa）
Chain C
26–1147（1122 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.56 Å |
| 8C89 SARS-CoV-2 spike in complex with the 17T2 neutralizing antibody Fab fragment (local refinement of RBD and Fab) Deposited 2023-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
324–533（210 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.41 Å |
| 8C8P Structure of the SARS-CoV-2 spike glycoprotein in complex with the 10D12 heavy-chain-only antibody (local refinement) Deposited 2023-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM Tris pH 8, 150 mM NaCl.
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8CBD SARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 1000
|
Resolution 3.52 Å R-free 0.266 |
| 8CBD SARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain Y
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 1000
|
Resolution 3.52 Å R-free 0.266 |
| 8CBD SARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain X
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 1000
|
Resolution 3.52 Å R-free 0.266 |
| 8CBE SARS-CoV-2 Delta-RBD complexed with BA.4/5-2 and Beta-49 Fabs Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M sodium citrate tribasic dihydrate pH 5.0 and 18% (w/v) PEG 20000
|
Resolution 3.16 Å R-free 0.266 |
| 8CBF SARS-CoV-2 Delta-RBD complexed with Omi-42 and Beta-49 Fabs Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 3 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；containing 0.1 M sodium citrate tribasic dihydrate pH 5.5 and 22% (w/v) PEG 1000
|
Resolution 2.33 Å R-free 0.255 |
| 8CII Delta-RBD complex with BA.2-07 fab, SARS1-34 fab and C1 nanobody Deposited 2023-02-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
327–528（202 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8CIM BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN Deposited 2023-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8CIN BA.4/5-5 FAB IN COMPLEX WITH SARS-COV-2 BA.4 SPIKE GLYCOPROTEIN Deposited 2023-02-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
28–1147（1120 aa）
Chain B
28–1147（1120 aa）
Chain C
28–1147（1120 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8CMA SARS-CoV-2 Delta-RBD complexed with BA.4/5-35 Fab Deposited 2023-02-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium citrate tribasic dihydrate pH 5.5, 18% w/v Polyethylene glycol 3,350
|
Resolution 3.29 Å R-free 0.268 |
| 8CMB Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S486-505 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
486–505（20 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 10 DHL 2-AMINO-ETHANETHIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1 M MES pH 6.0, 20 % PEG1500
|
Resolution 1.84 Å R-free 0.231 |
| 8CMC Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S511-530 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
511–530（20 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 15 SO4 SULFATE ION × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M MES pH 7.0, 25 % PEG8000, 0.2 M (NH4)2SO4
|
Resolution 1.42 Å R-free 0.208 |
| 8CMD Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S761-775 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
761–775（15 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；0.1 M MES pH 5.0, 20 % PEG1500
|
Resolution 2.54 Å R-free 0.238 |
| 8CMD Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S761-775 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
761–775（15 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；0.1 M MES pH 5.0, 20 % PEG1500
|
Resolution 2.54 Å R-free 0.238 |
| 8CMD Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Spike peptide S761-775 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
761–775（15 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；0.1 M MES pH 5.0, 20 % PEG1500
|
Resolution 2.54 Å R-free 0.238 |
| 8CMH Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S486-505 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
486–505（20 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 30 SO4 SULFATE ION × 1 DHL 2-AMINO-ETHANETHIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；0.1 M Sodium cacodylate pH 6.0, 25 % PEG4000, 0.2 M ammonium sulphate
|
Resolution 1.64 Å R-free 0.208 |
| 8CMI Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S761-775 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
761–775（15 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M TRIS pH 7.0, 28 % PEG8000, 0.2 M ammonium sulphate
|
Resolution 2.60 Å R-free 0.236 |
| 8CMI Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S761-775 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
761–775（15 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M TRIS pH 7.0, 28 % PEG8000, 0.2 M ammonium sulphate
|
Resolution 2.60 Å R-free 0.236 |
| 8CMI Human Leukocyte Antigen class II allotype DR1 presenting SARS-CoV-2 Omicron (BA.1) Spike peptide S761-775 Deposited 2023-02-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
761–775（15 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.1 M TRIS pH 7.0, 28 % PEG8000, 0.2 M ammonium sulphate
|
Resolution 2.60 Å R-free 0.236 |
| 8CSA Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 3-RBD-Down conformation (S-GSAS-D614G-K417N-E484K-N501Y) Deposited 2022-05-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N501Y; K417N; E484K; D614G; esidues 682-685 RRAR mutated to GSAS Mutation：N501Y; K417N; E484K; D614G; esidues 682-685 RRAR mutated to GSAS Mutation：N501Y; K417N; E484K; D614G; esidues 682-685 RRAR mutated to GSAS | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.84 Å |
| 8CSJ Cryo-EM structure of NTD-directed non-neutralizing antibody 4-33 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2022-05-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 8CWI Fab arm of antibody 10G4 bound to CoV-2 receptor binding domain (RBD) Deposited 2022-05-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–528（196 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | MG MAGNESIUM ION × 2 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；Equal volumes (0.4 uL) of protein solution (~5 mg/mL in 25 mM Tris (pH 8.0), 200 mM NaCl) were combined with well solution (200 mM MgCl2, 100 mM sodium acetate (pH 5.0), 20 % (w/v) PEG6000) in a sitting drop format.
|
Resolution 1.87 Å R-free 0.205 |
| 8CWK Fab arm of antibodies 4G1-C2 and 10G4 bound to CoV-2 receptor binding domain (RBD) Deposited 2022-05-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
333–528（196 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；Equal volume (2 uL) of protein solution (approx 5 mg/mL, in 25 mM Tris (pH 8.0), 200 mM NaCl) was mixed with an equal volume of well solution comprising 200 mM sodium citrate, 100 mM Bis-Tris-Propane (pH 7.4), 18% PEG3350). For cryoprotection the crystal was swum briefly (5-10 sec) in well solution doped with glycerol to a final concentration of ~25%.
|
Resolution 2.37 Å R-free 0.223 |
| 8CWU Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 1-21 Deposited 2022-05-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 10.5；293 K；20% polyethylene glycol 8000, 0.1 M NaCl, 0.1 M CAPS pH 10.5
|
Resolution 1.71 Å R-free 0.203 |
| 8CWV Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with a cross-neutralizing nanobody 2-31 and a human antibody CC12.1 Fab Deposited 2022-05-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；40% MPD, 0.1M cacodylate pH 6.5 5% (w/v) PEG-8000, final pH 7.0
|
Resolution 2.51 Å R-free 0.264 |
| 8CXN SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-57 Deposited 2022-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8CXQ SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-22 Deposited 2022-05-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 8CY6 SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-65 Deposited 2022-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8CY7 SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34 Deposited 2022-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 50 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8CY9 SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-23 Deposited 2022-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8CYA SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-67 Deposited 2022-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8CYB SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-8 Deposited 2022-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 AH2 1-deoxy-alpha-D-mannopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8CYC SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-34 Deposited 2022-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8CYD SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-45 Deposited 2022-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
15–1147（1133 aa）
Chain B
15–1147（1133 aa）
Chain C
15–1147（1133 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8CYJ RBD of SARS-CoV-2 Spike protein in complex with pan-sarbecovirus nanobodies 2-10, 2-67, 2-62 and 1-25 Deposited 2022-05-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8CZI Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with extended HR2 Deposited 2022-05-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1157–1201（45 aa）
Chain E
1157–1201（45 aa）
Chain F
1157–1201（45 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.22 Å |
| 8D0Z S728-1157 IgG in complex with SARS-CoV-2-6P-Mut7 Spike protein (focused refinement) Deposited 2022-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 11 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent (LMNG) added shortly before vitrification
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8D36 Crystal structure of SARS-CoV-2 fusion peptide in complex with neutralizing antibody COV44-62 Deposited 2022-05-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
812–826（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4；293.15 K；0.1 M sodium citrate, pH 4, 1 M lithium chloride, and 10% PEG6000
|
Resolution 1.45 Å R-free 0.219 |
| 8D47 fp.006 Fab in complex with SARS-CoV-2 Fusion Peptide Deposited 2022-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
812–831（20 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；289 K；0.2 M Potassium phosphate monobasic, 20% w/v Polyethylene glycol 3350
|
Resolution 2.00 Å R-free 0.238 |
| 8D47 fp.006 Fab in complex with SARS-CoV-2 Fusion Peptide Deposited 2022-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
812–831（20 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 2 PO4 PHOSPHATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.8；289 K；0.2 M Potassium phosphate monobasic, 20% w/v Polyethylene glycol 3350
|
Resolution 2.00 Å R-free 0.238 |
| 8D48 sd1.040 Fab in complex with SARS-CoV-2 Spike 2P glycoprotein Deposited 2022-06-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8D55 Closed state of SARS-CoV-2 BA.2 variant spike protein Deposited 2022-06-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8D56 One RBD-up state of SARS-CoV-2 BA.2 variant spike protein Deposited 2022-06-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8D5A Middle state of SARS-CoV-2 BA.2 variant spike protein Deposited 2022-06-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8D6Z Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV91-27 Deposited 2022-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
809–823（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；70% 2-methyl-2,4-pentanediol and 0.1M HEPES, pH 7.5
|
Resolution 2.30 Å R-free 0.279 |
| 8D6Z Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV91-27 Deposited 2022-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
809–823（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；70% 2-methyl-2,4-pentanediol and 0.1M HEPES, pH 7.5
|
Resolution 2.30 Å R-free 0.279 |
| 8D6Z Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV91-27 Deposited 2022-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
809–823（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；70% 2-methyl-2,4-pentanediol and 0.1M HEPES, pH 7.5
|
Resolution 2.30 Å R-free 0.279 |
| 8D6Z Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV91-27 Deposited 2022-06-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
809–823（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；70% 2-methyl-2,4-pentanediol and 0.1M HEPES, pH 7.5
|
Resolution 2.30 Å R-free 0.279 |
| 8D8Q SARS-CoV-2 Spike RBD in complex with DMAbs 2130 and 2196 Deposited 2022-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
16–1175（1160 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 8D8R SARS-CoV-2 Spike RBD in complex with DMAb 2196 Deposited 2022-06-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1175（1160 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8DAD SARS-CoV-2 receptor binding domain in complex with AZ090 Fab Deposited 2022-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1213（1213 aa）
Fragment：Spike 6P
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 8DAO Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79 Deposited 2022-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain I
809–823（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1 M Tris, pH 8.5, 0.01 M nickel (II) chloride, and 20% PEG monomethyl ether 2000
|
Resolution 2.80 Å R-free 0.284 |
| 8DAO Crystal structure of SARS-CoV-2 spike stem fusion peptide in complex with neutralizing antibody COV44-79 Deposited 2022-06-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain J
809–823（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293.15 K；0.1 M Tris, pH 8.5, 0.01 M nickel (II) chloride, and 20% PEG monomethyl ether 2000
|
Resolution 2.80 Å R-free 0.284 |
| 8DCC SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 3 Bound to P2B-2F6 Fab Deposited 2022-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
Fragment：RBD SPEEDesign Immunogen 3 (UNP residues 333-526)
|
Mutation：T333K, A363Y, N388K, N394Y, I468T, S514T, H519D, A522P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；291 K；0.2 M sodium fluoride, 20% w/v PEG3350
|
Resolution 2.60 Å R-free 0.272 |
| 8DCE SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv Deposited 2022-06-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–526（194 aa）
Fragment：RBD SPEEDesign Immunogen 1 (UNP residues 333-526)
|
Mutation：T333M,A348P,V362Y,A363Y,N394Q,Y396F,I468T,H519D,A522P | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.04 M potassium dihydrogen phosphate, 16% PEG8000, 20% glycerol
|
Resolution 2.00 Å R-free 0.203 |
| 8DF5 SARS-CoV-2 Beta RBD in complex with human ACE2 and S304 Fab and S309 Fab Deposited 2022-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain R
328–529（202 aa）
Chain S
328–529（202 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 30 CL CHLORIDE ION × 22 ZN ZINC ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M Tris (base)/bicine pH 8.5, 3% w/v D- sorbitol
|
Resolution 2.70 Å R-free 0.217 |
| 8DGU Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC25.106 isolated from a vaccinated COVID-19 convalescent Deposited 2022-06-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1140–1164（25 aa）
Fragment：Stem helix peptide, residues 1140-1164
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；19% (v/v) Isopropanol, 19% (w/v) PEG 4000, 5% (v/v) Glycerol, 0.095 M Sodium citrate pH 5.6
|
Resolution 1.89 Å R-free 0.245 |
| 8DI5 Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with VH domain F6 (focused refinement of RBD and VH F6) Deposited 2022-06-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8DLI Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.56 Å |
| 8DLJ Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human ACE2 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.91 Å |
| 8DLK Cryo-EM structure of SARS-CoV-2 Alpha (B.1.1.7) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8DLL Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.56 Å |
| 8DLM Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with human ACE2 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 8DLN Cryo-EM structure of SARS-CoV-2 Beta (B.1.351) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8DLO Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.25 Å |
| 8DLP Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human ACE2 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8DLQ Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8DLR Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8 (focused refinement of NTD and 4-8) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.51 Å |
| 8DLS Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 8DLT Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.40 Å |
| 8DLU Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human ACE2 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 8DLV Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 8DLW Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with Fab S2M11 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.16 Å |
| 8DLX Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.45 Å |
| 8DLY Cryo-EM structure of SARS-CoV-2 Epsilon (B.1.429) spike protein in complex with VH ab6 (focused refinement of NTD and VH ab6) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8DLZ Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：D614G Mutation：D614G Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.57 Å |
| 8DM0 Cryo-EM structure of SARS-CoV-2 D614G spike protein in complex with VH ab6 (focused refinement of NTD and VH ab6) Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Mutation：D614G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 8DM1 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8DM2 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein (focused refinement of NTD) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.91 Å |
| 8DM3 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with Fab 4A8 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.37 Å |
| 8DM4 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with Fab 4A8 (focused refinement of NTD and 4A8) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.45 Å |
| 8DM5 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with human ACE2 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.51 Å |
| 8DM6 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8DM7 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.49 Å |
| 8DM8 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2 (focused refinement of RBD and ACE2) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.68 Å |
| 8DM9 Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2 Deposited 2022-07-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.56 Å |
| 8DMA Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with mouse ACE2 (focused refinement of RBD and ACE2) Deposited 2022-07-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 8DNN Crystal structure of neutralizing antibody 80 in complex with SARS-CoV-2 receptor binding domain Deposited 2022-07-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
319–541（223 aa）
Chain D
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M di-ammonium tartarate, 20% (w/v) polyethylene glycol 3350
|
Resolution 3.12 Å R-free 0.252 |
| 8DPZ Local refinement of SARS-CoV-2 vaccine induced antibody DH1338 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain Deposited 2022-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
326–530（205 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.38 Å |
| 8DT3 Cryo-EM structure of spike binding to Fab of neutralizing antibody (locally refined) Deposited 2022-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8DT8 LM18/Nb136 bispecific tetra-nanobody immunoglobulin in complex with SARS-CoV-2-6P-Mut7 S protein (focused refinement) Deposited 2022-07-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Detergent added shortly to grid application
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.34 Å |
| 8DTK Structure of RBD directed antibody DH1047 in complex with SARS-CoV-2 spike: Local refinement of RBD-Fab interace Deposited 2022-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.77 Å |
| 8DTR Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV30-14 Deposited 2022-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
1145–1159（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1M sodium cacodylate, pH6.5, 0.2M sodium chloride, and 2M ammonium sulfate
|
Resolution 1.50 Å R-free 0.222 |
| 8DTR Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV30-14 Deposited 2022-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
1145–1159（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1M sodium cacodylate, pH6.5, 0.2M sodium chloride, and 2M ammonium sulfate
|
Resolution 1.50 Å R-free 0.222 |
| 8DTT Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV93-03 Deposited 2022-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
1148–1162（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.2M sodium chloride, 0.1M Tris, pH7, 30% PEG3000
|
Resolution 1.75 Å R-free 0.225 |
| 8DTT Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV93-03 Deposited 2022-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
1148–1162（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；0.2M sodium chloride, 0.1M Tris, pH7, 30% PEG3000
|
Resolution 1.75 Å R-free 0.225 |
| 8DTX Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV89-22 Deposited 2022-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
1145–1159（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；0.1 M sodium citrate, pH 5.6, 20% 2-propanol, and 20% PEG4000
|
Resolution 1.60 Å R-free 0.210 |
| 8DTX Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody COV89-22 Deposited 2022-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
1145–1159（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293.15 K；0.1 M sodium citrate, pH 5.6, 20% 2-propanol, and 20% PEG4000
|
Resolution 1.60 Å R-free 0.210 |
| 8DV1 SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432 Deposited 2022-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8DV2 SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to computationally engineered ACE2 mimetic CVD293 Deposited 2022-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8DW2 Cryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV-2 DARPin,SR22, and two antibody Fabs, S309 and CR3022 Deposited 2022-07-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
330–526（197 aa）
Fragment：receptor binding domain (UNP residues 330-526)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；10 mM HEPES, 7.4, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.11 Å |
| 8DW3 Cryo-EM structure of SARS-CoV-2 RBD in complex with anti-SARS-CoV-2 DARPin,SR16m, and two antibody Fabs, S309 and CR3022 Deposited 2022-07-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
330–526（197 aa）
Fragment：receptor binding domain (UNP residues 330-526)
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；10 mM HEPES, 7.4, 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.26 Å |
| 8DW9 Crystal structure of neutralizing antibody D29 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD) Deposited 2022-08-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
Fragment：receptor binding domain (UNP residues 333-527)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2 M ammonium sulfate, 0.05 M MES, pH 6.0, 5 mM magnesium acetate tetrahydrate
|
Resolution 4.00 Å R-free 0.381 |
| 8DW9 Crystal structure of neutralizing antibody D29 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD) Deposited 2022-08-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–527（195 aa）
Fragment：receptor binding domain (UNP residues 333-527)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2 M ammonium sulfate, 0.05 M MES, pH 6.0, 5 mM magnesium acetate tetrahydrate
|
Resolution 4.00 Å R-free 0.381 |
| 8DWA Crystal structure of neutralizing antibody P1D9 Fab in complex with SARS-CoV-2 spike receptor binding domain (RBD) Deposited 2022-08-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
335–515（181 aa）
Fragment：receptor binding domain (UNP residues 335-515)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 18% w/v PEG5000 MME
|
Resolution 3.20 Å R-free 0.297 |
| 8DXS Cryo-EM structure of RBD-directed neutralizing antibody P2B4 in complex with prefusion SARS-CoV-2 spike glycoprotein Deposited 2022-08-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 44 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.76 Å |
| 8DXT Fab arm of antibody GAR12 bound to the receptor binding domain of SARS-CoV-2. Deposited 2022-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；An equal volume (2 uL) of protein solution at ~5 mg/mL (in 25 mM Tris (pH 8.0), 200 mM NaCl) was combined with well solution (100 mM ammonium citrate (pH 5.5), 20% (w/v) PEG3350.
|
Resolution 2.25 Å R-free 0.254 |
| 8DXU Fab arms of antibodies GAR03 and 10G4 bound to the receptor binding domain of SARS-CoV-2 in a 1:1:1 complex. Deposited 2022-08-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
333–528（196 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Two uL of protein solution (~5 mg/mL of 1:1:1 complex in 25 mM Tris (pH 8.0), 200 mM NaCl) was combined with an equal volume of well solution (100 mM MMT buffer system (Molecular Dimensions) (pH 6.0), 19% (w/v) PEG6000.
|
Resolution 2.73 Å R-free 0.269 |
| 8DZH Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with two RBDs down in complex with the Fab fragment of human neutralizing antibody MB.02 Deposited 2022-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8DZI Structure of SARS-CoV-2 Omicron BA.1.1.529 Spike trimer with one RBD down in complex with the Fab fragment of human neutralizing antibody MB.02 Deposited 2022-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8E1G SARS-CoV-2 RBD in complex with Omicron-neutralizing antibody 2A10 Deposited 2022-08-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–591（273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1 uL 7.4 mg/mL protein; 1 uL 23%w/v PEG 3350, 230 mM Ammonium fluoride
|
Resolution 2.57 Å R-free 0.244 |
| 8E1G SARS-CoV-2 RBD in complex with Omicron-neutralizing antibody 2A10 Deposited 2022-08-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–591（273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1 uL 7.4 mg/mL protein; 1 uL 23%w/v PEG 3350, 230 mM Ammonium fluoride
|
Resolution 2.57 Å R-free 0.244 |
| 8EDF Bovine Fab SKD in complex with Sars COV-2 receptor binding domain Deposited 2022-09-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.2；293.15 K；0.4M Lithium chloride, 10% Peg6000, 0.1M sodium citrate
|
Resolution 3.40 Å R-free 0.299 |
| 8EKD Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike in complex with 2130-1-0114-112 Deposited 2022-09-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
333–516（184 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8EL2 SARS-CoV-2 RBD bound to neutralizing antibody Fab ICO-hu23 Deposited 2022-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | GOL GLYCEROL × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；10% PEG 8000, 0.1 M MES at pH 5.5, 0.2 M zinc acetate, 3% ethylene glycol, 3% glycerol, 10 mM cadmium chloride hydrate, 4% v/v polypropylene glycol P 400, 3% v/v 2-propanol
|
Resolution 2.89 Å R-free 0.281 |
| 8EL2 SARS-CoV-2 RBD bound to neutralizing antibody Fab ICO-hu23 Deposited 2022-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–541（223 aa）
|
Not recorded | GOL GLYCEROL × 1 ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；10% PEG 8000, 0.1 M MES at pH 5.5, 0.2 M zinc acetate, 3% ethylene glycol, 3% glycerol, 10 mM cadmium chloride hydrate, 4% v/v polypropylene glycol P 400, 3% v/v 2-propanol
|
Resolution 2.89 Å R-free 0.281 |
| 8ELH Crystal Structure of HLA-B*15:01 in complex with spike derived peptide NQKLIANQF from SARS-CoV-2 virus Deposited 2022-09-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
919–927（9 aa）
Fragment：NQK-OC43 peptide (UNP residues 919-927)
|
Not recorded | ACT ACETATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M sodium formate, pH 7.0, 20% w/v PEG3350
|
Resolution 1.85 Å R-free 0.223 |
| 8ELJ SARS-CoV-2 spike glycoprotein in complex with the ICO-hu23 neutralizing antibody Fab fragment Deposited 2022-09-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
13–1211（1199 aa）
Chain B
13–1211（1199 aa）
Chain C
13–1211（1199 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8ELO Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with antibody CC12.1 Fab and nanobody Nb-C4-225 Deposited 2022-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG-3350, 0.2 M di-Ammonium citrate
|
Resolution 2.72 Å R-free 0.261 |
| 8ELP Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with antibody CC12.1 Fab and nanobody Nb-C4-240 Deposited 2022-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.16 M ammonium sulfate, 0.08 M sodium acetate pH 4.6, 20% (w/v) polyethylene glycol 4000, 20% (v/v) glycerol
|
Resolution 2.83 Å R-free 0.284 |
| 8ELQ Crystal structure of SARS-CoV-2 spike protein receptor-binding domain in complex with antibody CC12.1 Fab and nanobody Nb-C4-255 Deposited 2022-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 25% (w/v) polyethylene glycol 4000
|
Resolution 2.21 Å R-free 0.285 |
| 8EOO Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibodies WRAIR-2063 and WRAIR-2151 Deposited 2022-10-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Bis-Tris propane HCl pH 8.5, 200 mM Na malonate dibasic, 20% w/v PEG 3350
|
Resolution 2.77 Å R-free 0.255 |
| 8EOO Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing human antibodies WRAIR-2063 and WRAIR-2151 Deposited 2022-10-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain D
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | GOL GLYCEROL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；100 mM Bis-Tris propane HCl pH 8.5, 200 mM Na malonate dibasic, 20% w/v PEG 3350
|
Resolution 2.77 Å R-free 0.255 |
| 8EPN Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 in the 3-RBD Down conformation Deposited 2022-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10mM Tris + 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8EPP Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs in the open conformation Deposited 2022-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10mM Tris + 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8EPQ Cryo-EM structure of SARS-CoV-2 Spike trimer S2D14 with two RBDs exposed Deposited 2022-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
27–1147（1121 aa）
Chain B
27–1147（1121 aa）
Chain C
27–1147（1121 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10mM Tris + 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8EQF cryoEM structure of a broadly neutralizing anti-SARS-CoV-2 antibody STI-9167 Deposited 2022-10-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 8ERQ SARS-CoV-2 BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment (local refinement of the RBD and S2X324) Deposited 2022-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–210（210 aa）
Chain A
212–1207（996 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8ERR SARS-CoV-2 Omicron BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment Deposited 2022-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–210（210 aa）
Chain A
212–1207（996 aa）
Chain B
1–210（210 aa）
Chain B
212–1207（996 aa）
Chain C
1–210（210 aa）
Chain C
212–1207（996 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8EYG SARS-CoV-2 spike protein complexed with two nanobodies Deposited 2022-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1149（1136 aa）
Chain B
14–1149（1136 aa）
Chain C
14–1149（1136 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；Wait time 20 seconds and blot time 3 seconds
|
Resolution 3.73 Å |
| 8EYH SARS-CoV-2 spike protein bound with a nanobody Deposited 2022-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1149（1136 aa）
Chain B
14–1149（1136 aa）
Chain C
14–1149（1136 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å |
| 8F0G Structure of SARS-CoV-2 Omicron BA.1 spike in complex with antibody Fab 1C3 Deposited 2022-11-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；TBS buffer pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 8F0H Structure of SARS-CoV-2 spike with antibody Fabs 2A10 and 1H2 (Local refinement of the RBD and Fabs 1H2 and 2A10) Deposited 2022-11-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；TBS buffer pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 8F0I Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody COVA309-22 Deposited 2022-11-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M sodium cacodylate, pH 6.5, 0.2 M magnesium chloride, and 20% (w/v) polyethylene glycol 1000
|
Resolution 3.70 Å R-free 0.275 |
| 8F0I Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody COVA309-22 Deposited 2022-11-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M sodium cacodylate, pH 6.5, 0.2 M magnesium chloride, and 20% (w/v) polyethylene glycol 1000
|
Resolution 3.70 Å R-free 0.275 |
| 8F0I Crystal structure of SARS-CoV-2 receptor binding domain in complex with human antibody COVA309-22 Deposited 2022-11-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；0.1 M sodium cacodylate, pH 6.5, 0.2 M magnesium chloride, and 20% (w/v) polyethylene glycol 1000
|
Resolution 3.70 Å R-free 0.275 |
| 8F2J Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2022-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3350
|
Resolution 3.16 Å R-free 0.245 |
| 8F2J Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2022-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3350
|
Resolution 3.16 Å R-free 0.245 |
| 8F2J Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2022-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3350
|
Resolution 3.16 Å R-free 0.245 |
| 8F2J Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2022-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；8% v/v Tacsimate pH 5.0, 20% w/v Polyethylene glycol 3350
|
Resolution 3.16 Å R-free 0.245 |
| 8F2X Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain Deposited 2022-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.12 M alcohol mixture (1,6-Hexanediol; 1-Butanol; 1,2-Propanediol; 2-Propanol; 1,4-Butanediol; 1,3-Propanediol), 0.1M buffer system 3 (Tris base and BICINE, pH 8.5), 50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) and 0.1 M Manganese(II) chloride tetrahydrate.
|
Resolution 3.50 Å R-free 0.324 |
| 8F4P SARS-CoV-2 spike protein trimer (down conformation) bound with a nanobody Deposited 2022-11-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1149（1136 aa）
Chain B
14–1149（1136 aa）
Chain C
14–1149（1136 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8FA1 Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with N969K mutation Deposited 2022-11-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain D
1157–1201（45 aa）
Chain E
1157–1201（45 aa）
Chain F
1157–1201（45 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.51 Å |
| 8FA2 Cryo-EM structure of the SARS-CoV-2 Omicron HR1-42G complex Deposited 2022-11-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
917–988（72 aa）
Chain B
917–988（72 aa）
Chain C
917–988（72 aa）
Chain D
1157–1201（45 aa）
Chain E
1157–1201（45 aa）
Chain F
1157–1201（45 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.82 Å |
| 8FAH Crystal structure of SARS-CoV-2 receptor binding domain in complex with SARS-CoV-2 reactive human antibody CR3022 Deposited 2022-11-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；1M Succinic acid, 0.1M HEPES pH 7.0 and 2% PEG MME2000
|
Resolution 4.22 Å R-free 0.286 |
| 8FDW Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane Deposited 2022-12-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
686–1273（588 aa）
Chain B
686–1273（588 aa）
Chain C
686–1273（588 aa）
|
Not recorded | MAN alpha-D-mannopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8FEZ Prefusion-stabilized SARS-CoV-2 spike protein Deposited 2022-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：N856L, A899Q, L916F, Y917W, T941D, A956L, K964E, D985N, P1143Q Mutation：N856L, A899Q, L916F, Y917W, T941D, A956L, K964E, D985N, P1143Q Mutation：N856L, A899Q, L916F, Y917W, T941D, A956L, K964E, D985N, P1143Q | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 8FHY Crystal structure of the SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5021 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | GOL GLYCEROL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350
|
Resolution 2.53 Å R-free 0.256 |
| 8FHY Crystal structure of the SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5021 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | GOL GLYCEROL × 7 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350
|
Resolution 2.53 Å R-free 0.256 |
| 8FHY Crystal structure of the SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5021 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | GOL GLYCEROL × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MLI MALONATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium malonate pH 7.0, 20% w/v Polyethylene glycol 3,350
|
Resolution 2.53 Å R-free 0.256 |
| 8FI9 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 0.1 M Phosphate-citrate pH 4.5, 20% w/v PEG 8000
|
Resolution 4.20 Å R-free 0.296 |
| 8FI9 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 0.1 M Phosphate-citrate pH 4.5, 20% w/v PEG 8000
|
Resolution 4.20 Å R-free 0.296 |
| 8FI9 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain O
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 0.1 M Phosphate-citrate pH 4.5, 20% w/v PEG 8000
|
Resolution 4.20 Å R-free 0.296 |
| 8FI9 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody WRAIR-5001 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 0.1 M Phosphate-citrate pH 4.5, 20% w/v PEG 8000
|
Resolution 4.20 Å R-free 0.296 |
| 8FU7 Structure of Covid Spike variant deltaN135 in fully closed form Deposited 2023-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1204（1204 aa）
Chain B
1–1204（1204 aa）
Chain C
1–1204（1204 aa）
|
Mutation：A892P, A942P, D614N,V987P Mutation：A892P, A942P, D614N,V987P Mutation：A892P, A942P, D614N,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 8FU8 Structure of Covid Spike variant deltaN135 with one erect RBD Deposited 2023-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：A892P,A942P,D614N,V987P Mutation：A892P,A942P,D614N,V987P Mutation：A892P,A942P,D614N,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å |
| 8FU9 Structure of Covid Spike variant deltaN25 with one erect RBD Deposited 2023-01-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：A892P,A942P,V987P,D614N,D253N,L452Q,F490S,T859N Mutation：A892P,A942P,V987P,D614N,D253N,L452Q,F490S,T859N Mutation：A892P,A942P,V987P,D614N,D253N,L452Q,F490S,T859N | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 8FXB SARS-CoV-2 XBB.1 spike RBD bound to the human ACE2 ectodomain and the S309 neutralizing antibody Fab fragment Deposited 2023-01-24 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
328–528（201 aa）
Fragment：Receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8FXC SARS-CoV-2 BQ.1.1 spike RBD bound to the human ACE2 ectodomain and the S309 neutralizing antibody Fab fragment Deposited 2023-01-24 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
328–528（201 aa）
Fragment：Receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8G70 SARS-CoV-2 spike/nanobody mixture complex Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8G71 Spike/Nb2 complex with 1 RBD up Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.10 Å |
| 8G72 SARS-CoV-2 spike/Nb2 complex with 1 RBD up (local refinement at 5.6 A) Deposited 2023-02-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
14–1211（1198 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.60 Å |
| 8G73 SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 bound at 2.5 A Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 8G74 SARS-CoV-2 spike/Nb3 complex with 1 RBD up and 2 Nb3 Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 8G75 SARS-CoV-2 spike/Nb4 complex with 2 RBDs up and 3 Nb4 bound Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8G76 SARS-CoV-2 spike/Nb5 complex Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8G77 SARS-CoV-2 spike/Nb6 complex Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8G78 Local refinement of SARS-CoV-2 spike/nanobody mixture complex around NTD Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8G79 Local refinement of SARS-CoV-2 spike/nanobody mixture complex around RBD Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.10 Å |
| 8G7A SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 (local refinement) Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8G7B SARS-CoV-2 spike/Nb3 complex with 1 RBD up and 2 Nb3 (local refinement) Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8G7C local refinement of SARS-CoV-2 spike/Nb4 complex with 2 RBDs up and 3 Nb4 bound Deposited 2023-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8GB0 SARS-CoV-2 Spike H655Y variant, One RBD Open Deposited 2023-02-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 8GB5 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9 Deposited 2023-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | SO4 SULFATE ION × 1 BCN BICINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；1.6 M ammonium sulfate, 0.1 M bicine pH 9, and 15% glycerol
|
Resolution 3.35 Å R-free 0.320 |
| 8GB5 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9 Deposited 2023-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | SO4 SULFATE ION × 3 BCN BICINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；1.6 M ammonium sulfate, 0.1 M bicine pH 9, and 15% glycerol
|
Resolution 3.35 Å R-free 0.320 |
| 8GB5 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9 Deposited 2023-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | SO4 SULFATE ION × 1 BCN BICINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；1.6 M ammonium sulfate, 0.1 M bicine pH 9, and 15% glycerol
|
Resolution 3.35 Å R-free 0.320 |
| 8GB5 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 25F9 Deposited 2023-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | SO4 SULFATE ION × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；1.6 M ammonium sulfate, 0.1 M bicine pH 9, and 15% glycerol
|
Resolution 3.35 Å R-free 0.320 |
| 8GB6 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 21B6 Deposited 2023-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | SO4 SULFATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3.3；298.15 K；0.1 M sodium citrate, pH 3.3 and 1.45 M ammonium sulfate
|
Resolution 1.75 Å R-free 0.221 |
| 8GB7 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody 20A7 Deposited 2023-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.2 M CaCl2, 10% ethylene glycol (v/v), and 20% polyethylene glycol 3350 (w/v)
|
Resolution 2.57 Å R-free 0.245 |
| 8GB8 Crystal structure of SARS-CoV-2 BA.2 receptor binding domain in complex with neutralizing antibody 20A7 Deposited 2023-02-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–541（223 aa）
Fragment：Receptor binding domain, UNP residues 319-541
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 GLY GLYCINE × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1 M HEPES pH 7.5, 10% (v/v) glycerol, 5% (w/v) polyethylene glycol 3000, and
30% (v/v) polyethylene glycol 400
|
Resolution 2.30 Å R-free 0.228 |
| 8GDR SARS-Cov2 S protein structure in complex with neutralizing monoclonal antibody 002-S21B10 Deposited 2023-03-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
14–1149（1136 aa）
Chain E
14–1149（1136 aa）
Chain F
14–1149（1136 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8GF2 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies eCR3022.20 and CC12.3 Deposited 2023-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate - citric acid buffer pH 5.0, 15% (v/v) ethylene glycol, 1 M lithium chloride, and 10% (w/v) polyethylene glycol 6000
|
Resolution 2.85 Å R-free 0.252 |
| 8GF2 Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies eCR3022.20 and CC12.3 Deposited 2023-03-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate - citric acid buffer pH 5.0, 15% (v/v) ethylene glycol, 1 M lithium chloride, and 10% (w/v) polyethylene glycol 6000
|
Resolution 2.85 Å R-free 0.252 |
| 8GJM 17b10 fab in complex with full-length SARS-CoV-2 Spike G614 trimer Deposited 2023-03-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8GJN 17B10 fab in complex with up-RBD of SARS-CoV-2 Spike G614 trimer Deposited 2023-03-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–530（198 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8GNH Complex structure of BD-218 and Spike protein Deposited 2022-08-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；25mM Tris, pH 8.0, 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.74 Å |
| 8GOM SARS-CoV-2 specific private TCR RLQ7 in complex with RLQ-HLA-A2 Deposited 2022-08-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
1000–1008（9 aa）
Fragment：RLQ epitope
|
Not recorded | PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 0.01 M Trimethylamine hydrochloride, 15% PEG 6000.
|
Resolution 2.78 Å R-free 0.248 |
| 8GON SARS-CoV-2 specific private TCR RLQ7 in complex with RLQ-T1006I-HLA-A2 Deposited 2022-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
1000–1008（9 aa）
Fragment：RLQ mutant epitope
|
Mutation：T10006I | PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M Tris-HCl pH 8.5, 15% PEG 6000
|
Resolution 2.60 Å R-free 0.253 |
| 8GOU Omicron BA.4/5 SARS-CoV-2 S in complex with TH003 Fab Deposited 2022-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S,F817P, A892P, A899P,A942P K986P, V987P Mutation：R682G, R683S, R685S,F817P, A892P, A899P,A942P K986P, V987P Mutation：R682G, R683S, R685S,F817P, A892P, A899P,A942P K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8GPY Crystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv Deposited 2022-08-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Potassium formate, PEG 3350
|
Resolution 2.51 Å R-free 0.251 |
| 8GPY Crystal structure of Omicron BA.4/5 RBD in complex with a neutralizing antibody scFv Deposited 2022-08-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: trimeric |
Chain B
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；Potassium formate, PEG 3350
|
Resolution 2.51 Å R-free 0.251 |
| 8GRY Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with rat ACE2 (local refinement) Deposited 2022-09-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：RBD
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 8GS6 Structure of the SARS-CoV-2 BA.2.75 spike glycoprotein (closed state 1) Deposited 2022-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：R682G, R683S, R685G, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685G, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685G, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Octyl glucoside solution was added to PBS solution to a final concentration of 0.01%
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.86 Å |
| 8GS9 SARS-CoV-2 BA.2 spike RBD in complex bound with VacBB-551 Deposited 2022-09-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
337–517（181 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 5s, wait for 2s, blot force:0
|
Resolution 2.66 Å |
| 8GSB SARS-COV-2 BA.1 Spike incomplex with VacBB-665 Deposited 2022-09-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 5s, waiting for 2.5s, blot force 0
|
Resolution 3.99 Å |
| 8GTO cryo-EM structure of Omicron BA.5 S protein in complex with XGv282 Deposited 2022-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8GTP cryo-EM structure of Omicron BA.5 S protein in complex with XGv289 Deposited 2022-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8GTQ cryo-EM structure of Omicron BA.5 S protein in complex with S2L20 Deposited 2022-09-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8GX9 Crystal structure of SARS-CoV-2 RBD with P2C-1F11 and P2B-1G5 Deposited 2022-09-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
319–529（211 aa）
Chain E
319–529（211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M sodium chloride, 0.1M MES, pH 6.0, 20% PEG 2000 MME
|
Resolution 4.01 Å R-free 0.297 |
| 8GZ5 Crystal structure of neutralizing VHH P17 in complex with SARS-CoV-2 Alpha variant spike receptor-binding domain Deposited 2022-09-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–530（198 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 12 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M Bis-Tris propane pH 7.0, 1.0M succinic acid pH 7.0
|
Resolution 1.70 Å R-free 0.189 |
| 8GZZ Local refinement of SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab Deposited 2022-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
334–527（194 aa）
Fragment：SARS-CoV-2 Omicron BA.1 Spike glycoprotein receptor binding domain
Chain B
334–527（194 aa）
Fragment：SARS-CoV-2 Omicron BA.1 Spike glycoprotein receptor binding domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.52 Å |
| 8H00 SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab in the class 1 conformation Deposited 2022-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 8H01 SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 Fab in class 2 conformation Deposited 2022-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F819P, A892P, A899P, A942P Mutation：R682G, R683S, R685S, F819P, A892P, A899P, A942P Mutation：R682G, R683S, R685S, F819P, A892P, A899P, A942P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8H06 Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with human ACE2 (local refinement) Deposited 2022-09-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 8H07 SARS-CoV-2 BA.4 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C Deposited 2022-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8H08 SARS-CoV-2 BA.1 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C Deposited 2022-09-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8H3D Structure of apo SARS-CoV-2 spike protein with one RBD up Deposited 2022-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain B
1–1211（1211 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain C
1–1211（1211 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
|
Mutation：R682S,R683G,R685G,K986P,V987P Mutation：R682S,R683G,R685G,K986P,V987P Mutation：R682S,R683G,R685G,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 8H3E Complex structure of a small molecule (SPC-14) bound SARS-CoV-2 spike protein, closed state Deposited 2022-10-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain B
1–1211（1211 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain C
1–1211（1211 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
|
Mutation：R682S,R683G,R685G,K986P,V987P Mutation：R682S,R683G,R685G,K986P,V987P Mutation：R682S,R683G,R685G,K986P,V987P | Q83 7-(6-nitro-2,3-dihydroindol-1-yl)-7-oxidanyidene-heptanoic acid × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 8H3M Conformation 1 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab Deposited 2022-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1212（1212 aa）
Chain B
1–1212（1212 aa）
Chain C
1–1212（1212 aa）
|
Mutation：;D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F ; Mutation：;D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F ; Mutation：;D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F ; | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.48 Å |
| 8H3N Conformation 2 of SARS-CoV-2 Omicron BA.1 Variant Spike protein complexed with MO1 Fab Deposited 2022-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1212（1212 aa）
Chain B
1–1212（1212 aa）
Chain C
1–1212（1212 aa）
|
Mutation：;D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981 ; Mutation：;D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981 ; Mutation：;D614G, R682del, R683del, R685del, F817P, A892P, A899P, A942P, K986P, V987P A67V, H69del, V70del, T95I, G142D, V143del, Y144del, Y145del, N211del, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981 ; | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.73 Å |
| 8H5C Structure of SARS-CoV-2 Omicron BA.2.75 RBD in complex with human ACE2 Deposited 2022-10-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；0.15 M Ammonium sulfate, 0.1 M Sodium HEPES, 20 % w/v PEG 4000
|
Resolution 2.90 Å R-free 0.242 |
| 8H5T Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-015 Deposited 2022-10-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
320–537（218 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium formate, pH 7.2, 20% w/v polyethylene glycol 3350
|
Resolution 2.00 Å R-free 0.205 |
| 8H5U Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-021 Deposited 2022-10-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
320–537（218 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium citrate tribasic dihydrate, pH 5.0, 18% w/v polyethylene glycol 20000
|
Resolution 2.40 Å R-free 0.245 |
| 8H5U Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-021 Deposited 2022-10-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
320–537（218 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M sodium citrate tribasic dihydrate, pH 5.0, 18% w/v polyethylene glycol 20000
|
Resolution 2.40 Å R-free 0.245 |
| 8H6F Cryo-EM structure of SARS-CoV-2 Spike protein in complex with A6 repebody Deposited 2022-10-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K980P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K980P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K980P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20mM Tris-HCl, 200mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8H7L Cryo-EM Structure of SARS-CoV-2 BA.2 Spike protein in complex with BA7535 Deposited 2022-10-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
18–1143（1126 aa）
Chain B
18–1143（1126 aa）
Chain C
18–1143（1126 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.44 Å |
| 8H7Z Cryo-EM structure of SARS-CoV-2 BA.2 RBD in complex with BA7535 fab (local refinement) Deposited 2022-10-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–528（197 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 8H91 Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with nanobody N19 Deposited 2022-10-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
334–527（194 aa）
Chain B
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；1%(w/v) Tryptone, 0.001 M Sodiumazide, 0.05 M HepesSodium pH7.0, 20%(w/v) polyethyleneglycol3350
|
Resolution 3.07 Å R-free 0.284 |
| 8HC2 SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 1 YB9-258 Fab (1 RBD up) Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：671-674del,F817P,A892P,A899P,A942P,K976P,V977P Mutation：671-674del,F817P,A892P,A899P,A942P,K976P,V977P Mutation：671-674del,F817P,A892P,A899P,A942P,K976P,V977P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.21 Å |
| 8HC3 SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 2 YB9-258 Fabs (2 RBD up) Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.35 Å |
| 8HC4 SARS-CoV-2 wildtype spike trimer (6P) in complex with 3 YB9-258 Fabs and 3 R1-32 Fabs (3 RBD up) Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.54 Å |
| 8HC5 SARS-CoV-2 wildtype S1 in complex with YB9-258 Fab and R1-32 Fab Deposited 2022-11-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
1–676（676 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.43 Å |
| 8HC6 SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB9-258 Fab, focused refinement of Fab region Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
14–289（276 aa）
Chain C
322–588（267 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.69 Å |
| 8HC7 SARS-CoV-2 Omicron BA.1 spike trimer (6P) complex with YB9-258 Fab, focused refinement of RBD-dimer region Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
322–588（267 aa）
Chain C
14–526（513 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.54 Å |
| 8HC8 SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with YB13-292 Fab, focused refinement of Fab region Deposited 2022-11-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
332–517（186 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 8HC9 SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (3 RBD down) Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.03 Å |
| 8HCA SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (1 RBD up) Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.35 Å |
| 8HCB SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (2 RBD up) Deposited 2022-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.18 Å |
| 8HEB SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class 1 conformation Deposited 2022-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 8HEC SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab in the class 2 conformation Deposited 2022-11-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P Mutation：R682G, R683S, R685S, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8HED Local refinement of the SARS-CoV-2 Spike trimer in complex with RmAb 9H1 Fab Deposited 2022-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
331–530（200 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.59 Å |
| 8HES Crystal structure of SARS-CoV-2 RBD and NIV-10 complex Deposited 2022-11-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
322–536（215 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Sodium nitrate, 20% PEG 3350
|
Resolution 2.20 Å R-free 0.241 |
| 8HFX Cryo-EM structure of SARS-CoV-2 Omicron BA.1 spike protein in complex with white-tailed deer ACE2 Deposited 2022-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 8HFY SARS-CoV-2 Omicron BA.1 spike protein receptor-binding domain in complex with white-tailed deer ACE2 Deposited 2022-11-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 8HFZ Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with white-tailed deer ACE2 Deposited 2022-11-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1217（1217 aa）
Chain B
1–1217（1217 aa）
Chain C
1–1217（1217 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å |
| 8HG0 Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-binding domain in complex with white-tailed deer ACE2 Deposited 2022-11-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.51 Å |
| 8HGL SARS-CoV-2 spike in complex with neutralizing antibody NIV-11 Deposited 2022-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；octyl-maltoside, fluorinated solution was added to PBS solution to a final concentration of 0.03%
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.90 Å |
| 8HGM Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11 Deposited 2022-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；octyl-maltoside, fluorinated solution was added to PBS solution to a final concentration of 0.03%
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.40 Å |
| 8HHX SARS-CoV-2 Delta Spike in complex with FP-12A Deposited 2022-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Tris pH 7.5
150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 8HHY SARS-CoV-2 Delta Spike in complex with IS-9A Deposited 2022-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Tris pH 7.5
150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8HHZ SARS-CoV-2 Omicron BA.1 Spike in complex with IY-2A Deposited 2022-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1210（1197 aa）
Chain B
14–1210（1197 aa）
Chain C
14–1210（1197 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Tris pH 7.5
150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.28 Å |
| 8HLC S protein of SARS-CoV-2 in complex with 3711 Deposited 2022-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K986P,V987P Mutation：K986P,V987P Mutation：K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8HLD S protein of SARS-CoV-2 in complex with 26434 Deposited 2022-11-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8HN6 Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD Deposited 2022-12-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain E
333–527（195 aa）
Chain F
333–527（195 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG 3350,0.1 M HEPES,0.2 M LProline
|
Resolution 2.07 Å R-free 0.214 |
| 8HN7 Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD Deposited 2022-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG4000,magnesium chloride, HEPES
|
Resolution 3.00 Å R-free 0.263 |
| 8HN7 Crystal structure of monoclonal antibody complexed with SARS-CoV-2 RBD Deposited 2022-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；PEG4000,magnesium chloride, HEPES
|
Resolution 3.00 Å R-free 0.263 |
| 8HP9 Cryo-EM structure of SARS-CoV-2 Omicron BA.2 S-trimer in complex with fab L4.65 and L5.34 Deposited 2022-12-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 8HPF Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with fab L4.65 and L5.34 Deposited 2022-12-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
335–527（193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.34 Å |
| 8HPQ Cryo-EM structure of SARS-CoV-2 Omicron BA.4 S-trimer in complex with fab L4.65 and L5.34 Deposited 2022-12-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 8HPU Cryo-EM structure of SARS-CoV-2 Omicron BA.4 RBD in complex with fab L4.65 and L5.34 Deposited 2022-12-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.56 Å |
| 8HPV Cryo-EM structure of SARS-CoV-2 Omicron Prototype S-trimer in complex with fab L4.65 and L5.34 Deposited 2022-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
14–1147（1134 aa）
Chain B
14–1147（1134 aa）
Chain C
14–1147（1134 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 8HQ7 Cryo-EM structure of SARS-CoV-2 Omicron Prototype RBD in complex with fab L4.65 and L5.34 Deposited 2022-12-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–527（195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8HR2 Ternary Crystal Complex Structure of RBD with NB1B5 and NB1C6 Deposited 2022-12-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–523（191 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；293.15 K；0.2 mM HEPES pH7.0;12% PEG3350
|
Resolution 1.94 Å R-free 0.222 |
| 8HRD Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium formate, 20% w/v Polyethylene glycol 3350
|
Resolution 2.86 Å R-free 0.244 |
| 8HRD Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium formate, 20% w/v Polyethylene glycol 3350
|
Resolution 2.86 Å R-free 0.244 |
| 8HRD Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain K
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium formate, 20% w/v Polyethylene glycol 3350
|
Resolution 2.86 Å R-free 0.244 |
| 8HRD Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant in complex with IMCAS74 Fab and W14 Fab Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain T
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium formate, 20% w/v Polyethylene glycol 3350
|
Resolution 2.86 Å R-free 0.244 |
| 8HRI SARS-CoV-2 Delta variant spike protein Deposited 2022-12-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–1208（1194 aa）
Chain B
15–1208（1194 aa）
Chain C
15–1208（1194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8HRJ SARS-CoV-2 Delta variant spike protein Deposited 2022-12-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–1208（1194 aa）
Chain B
15–1208（1194 aa）
Chain C
15–1208（1194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8HRK SARS-CoV-2 Delta S-RBD-ACE2 complex Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8HRL SARS-CoV-2 Delta S-RBD-ACE2 Deposited 2022-12-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8HWS The complex structure of Omicron BA.4 RBD with BD604, S309, and S304 Deposited 2023-01-02 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.36 Å |
| 8HWT SARS-CoV-2 Omicron BA.2 RBD complexed with BD-604 and S304 Fab Deposited 2023-01-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.91 Å |
| 8HXJ BANAL-20-52 Spike trimer Deposited 2023-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8I3S Local CryoEM structure of the SARS-CoV-2 S6P in complex with 7B3 Fab Deposited 2023-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1213（1200 aa）
Fragment：RBD region
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8I3U Local CryoEM structure of the SARS-CoV-2 S6P in complex with 14B1 Fab Deposited 2023-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1213（1200 aa）
Fragment：RBD region
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8I4E Omicron spike variant XBB with Bn03 Deposited 2023-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
28–1208（1181 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.98 Å |
| 8I4F Omicron spike variant XBB with n3130v-Fc Deposited 2023-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
28–1208（1181 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 8I4G Omicron spike variant BQ.1.1 with n3130v-Fc Deposited 2023-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
28–1208（1181 aa）
|
Mutation：R682G, R683S, R685S | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.68 Å |
| 8I4H Omicron spike variant BA.1 with Bn03 Deposited 2023-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.81 Å |
| 8I5H Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
334–527（194 aa）
Fragment：Delta RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pH 6.5 100 mM Bis-Tris, 17.5% PEG 10K, 100 mM Ammonium acetate, 5% Glycerol
|
Resolution 2.38 Å R-free 0.230 |
| 8I5H Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
Fragment：Delta RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pH 6.5 100 mM Bis-Tris, 17.5% PEG 10K, 100 mM Ammonium acetate, 5% Glycerol
|
Resolution 2.38 Å R-free 0.230 |
| 8I5H Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG48 Fab Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
334–527（194 aa）
Fragment：Delta RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；pH 6.5 100 mM Bis-Tris, 17.5% PEG 10K, 100 mM Ammonium acetate, 5% Glycerol
|
Resolution 2.38 Å R-free 0.230 |
| 8I5I Crystal structure of SARS-CoV-2 delta variant spike receptor-binding domain (RBD) in complex with NCV2SG53 Fab Deposited 2023-01-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
321–536（216 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 1500
|
Resolution 3.06 Å R-free 0.372 |
| 8I9B S-ECD (Omicron BA.2.75) in complex with PD of ACE2 Deposited 2023-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1206（1206 aa）
Chain B
1–1206（1206 aa）
Chain C
1–1206（1206 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8I9C S-ECD (Omicron BF.7) in complex with PD of ACE2 Deposited 2023-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 8I9D S-ECD (Omicron XBB.1) in complex with PD of ACE2 Deposited 2023-02-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 8I9E S-RBD(Omicron BA.3) in complex with PD of ACE2 Deposited 2023-02-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8I9F S-RBD (Omicron BA.2.75) in complex with PD of ACE2 Deposited 2023-02-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8I9G S-RBD (Omicron BF.7) in complex with PD of ACE2 Deposited 2023-02-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8I9H S-RBD (Omicron XBB.1) in complex with PD of ACE2 Deposited 2023-02-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8IDN Cryo-EM structure of RBD/E77-Fab complex Deposited 2023-02-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
332–531（200 aa）
Fragment：Receptor binding domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.35 Å |
| 8IF2 Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BQ.1.1 variant spike protein in complex with its receptor ACE2 Deposited 2023-02-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
322–536（215 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；Sodium acetate, Ammonium acetate, PEG4000
|
Resolution 2.78 Å R-free 0.245 |
| 8IFY Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein in complex with white-tailed deer ACE2 Deposited 2023-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
28–1145（1118 aa）
Chain B
28–1145（1118 aa）
Chain C
28–1145（1118 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.55 Å |
| 8IFZ Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 spike protein receptor-binding domain in complex with white-tailed deer ACE2 Deposited 2023-02-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 8IOS Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-1 state) Deposited 2023-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.50 Å |
| 8IOT Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state) Deposited 2023-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.51 Å |
| 8IOU Structure of SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 (1-up state) Deposited 2023-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.18 Å |
| 8IOV Structure of SARS-CoV-2 XBB.1 spike RBD in complex with ACE2 Deposited 2023-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.29 Å |
| 8ITU SARS-CoV-2 Omicron BA.1 Spike glycoprotein in complex with rabbit monoclonal antibody 1H1 IgG. Deposited 2023-03-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.68 Å |
| 8IV4 Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 8H12 and 3E2 (local refinement) Deposited 2023-03-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
324–527（204 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.59 Å |
| 8IV5 Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 8H12 and 1C4 (local refinement) Deposited 2023-03-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
324–527（204 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.77 Å |
| 8IV8 Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs 3E2 and 1C4 (local refinement) Deposited 2023-03-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
324–527（204 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.92 Å |
| 8IVA Cryo-EM structure of SARS-CoV-2 spike protein in complex with double nAbs XMA01 and 3E2 (local refinement) Deposited 2023-03-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
324–527（204 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 8IX3 Cryo-EM structure of SARS-CoV-2 BA.4/5 spike protein in complex with 1G11 (local refinement) Deposited 2023-03-31 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
333–557（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.98 Å |
| 8J1Q CryoEM structure of SARS CoV-2 RBD and Aptamer complex Deposited 2023-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric |
Chain C
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；1mM MgCl2, 0.15% amphipol A8-35 and 0.003% cymal-6 additive added during sample preparation
cryo-EM vitrification conditions
Cryogen ETHANE；2.5 ul of samples placed on grid before plunge frozen with 5s blot time
|
Resolution 3.30 Å |
| 8J1T Local refined cryo-EM structure of Omicron BA.5 RBD in complex with 8-9D Fab Deposited 2023-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8J1V Cryo-EM structure of SARS-CoV2 Omicron BA.5 spike in complex with 8-9D Fabs Deposited 2023-04-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
25–1141（1117 aa）
Chain B
25–1141（1117 aa）
Chain E
25–1141（1117 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 8J26 CryoEM structure of SARS CoV-2 RBD and Aptamer complex Deposited 2023-04-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric |
Chain C
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；1mM MgCl2, 0.15% amphipol A8-35 and 0.003% cymal-6 additive added during sample preparation
cryo-EM vitrification conditions
Cryogen ETHANE；2.5 ul of samples placed on grid before plunge frozen with 5s blot time
|
Resolution 3.40 Å |
| 8JAP Cryo-EM structure of SARS-CoV-2 WT RBD in complex with W328-6H2 (local refinement) Deposited 2023-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–540（540 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.81 Å |
| 8JIN The local refined map of XBB spike protein (S) in complex with bispecific antibody G7-Fc Deposited 2023-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1208（1181 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.45 Å |
| 8JIO XBB spike protein (S) in complex with monoclonal antibody 6I18 Deposited 2023-05-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1208（1181 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8JJE RBD of SARS-CoV2 spike protein with ACE2 decoy Deposited 2023-05-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
14–1211（1198 aa）
|
Mutation：R682G,R683S,R685G,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8JMM Structure of XBB spike protein (S) dimer-trimer in complex with bispecific antibody G7-Fc at 3.75 Angstroms resolution. Deposited 2023-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
Chain D
28–1208（1181 aa）
Chain E
28–1208（1181 aa）
Chain F
28–1208（1181 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å |
| 8JVA Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N235 and S2L20 Fab Deposited 2023-06-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–303（303 aa）
Fragment：N-terminal
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 8JYK Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 1) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.59 Å |
| 8JYK Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 1) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.59 Å |
| 8JYK Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 1) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.59 Å |
| 8JYM Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.79 Å |
| 8JYM Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.79 Å |
| 8JYM Structure of the SARS-CoV-2 XBB.1.5 spike glycoprotein (closed state 2) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.79 Å |
| 8JYN Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (1-up state) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
28–1210（1183 aa）
Chain B
28–1210（1183 aa）
Chain C
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.04 Å |
| 8JYO Structure of SARS-CoV-2 XBB.1.5 spike glycoprotein in complex with ACE2 (2-up state) Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
28–1210（1183 aa）
Chain B
28–1210（1183 aa）
Chain C
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.20 Å |
| 8JYP Structure of SARS-CoV-2 XBB.1.5 spike RBD in complex with ACE2 Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.38 Å |
| 8JYS SARS-CoV-2 Spike RBD (dimer) in complex with two 2S-1244 nanobodies Deposited 2023-07-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
333–528（196 aa）
Chain D
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8K18 Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD Deposited 2023-07-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.68 Å |
| 8K19 Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD Deposited 2023-07-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.88 Å |
| 8K3K The crystal structure of nanobody Nb4 in complex with receptor binding domain (RBD) of BA.1 Spike protein Deposited 2023-07-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–531（213 aa）
Fragment：receptor binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M potassium thiocyanate, 20 %(w/v) PEG 3350
|
Resolution 2.43 Å R-free 0.269 |
| 8K45 A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains Deposited 2023-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 8K46 A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains Deposited 2023-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 8K47 A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses including all major Omicron strains Deposited 2023-07-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.54 Å |
| 8K5G Structure of the SARS-CoV-2 BA.1 RBD with UT28-RD Deposited 2023-07-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
325–549（225 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 8K5H Structure of the SARS-CoV-2 BA.1 spike with UT28-RD Deposited 2023-07-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.22 Å |
| 8K9B SARS-CoV-2 spike protein in complex with one S2H5 Fab Deposited 2023-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.50 Å |
| 8K9J SARS-CoV-2 spike protein in complex with two S2H5 Fabs on NTD-1 and NTD-2 Deposited 2023-08-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.60 Å |
| 8K9M SARS-CoV-2 spike protein in complex with two S2H5 Fabs on NTD-1 and NTD-3 Deposited 2023-08-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.80 Å |
| 8KA8 Cryo-EM structure of SARS-CoV-2 Delta RBD in complex with golden hamster ACE2 (local refinement) Deposited 2023-08-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 8KC2 Cryo-EM structure of SARS-CoV-2 BA.3 RBD in complex with golden hamster ACE2 (local refinement) Deposited 2023-08-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–526（194 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8KDR The local refined map of SARS-CoV-2 XBB Variant Spike protein complexed with antibody PW5-535 Deposited 2023-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8KEH State 2 of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5 Deposited 2023-08-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 8KEJ Monomer state of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5 Deposited 2023-08-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1208（1181 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.73 Å |
| 8KEO Structure of SARS-CoV-2 Omicron BA.1 Spike complexed with antibody PW5-570 Deposited 2023-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.78 Å |
| 8KEP The local refined map of SARS-CoV-2 Omicron BA.1 Spike complexed with antibody PW5-570 Deposited 2023-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 8KEQ State 1 of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5 Deposited 2023-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 8KER Structure of SARS-CoV-2 XBB Variant Spike protein complexed with broadly neutralizing antibody PW5-535 Deposited 2023-08-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 8KHC SARS-CoV-2 Omicron spike in complex with 5817 Fab Deposited 2023-08-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
27–1146（1120 aa）
Chain B
27–1146（1120 aa）
Chain C
27–1146（1120 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8KHD The interface structure of Omicron RBD binding to 5817 Fab Deposited 2023-08-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
330–530（201 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8OWT SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound Deposited 2023-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain BBB
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；NaCl, potassium citrate pH 4.2, PEG 8000
|
Resolution 2.37 Å R-free 0.249 |
| 8OWT SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound Deposited 2023-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain EEE
330–532（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；NaCl, potassium citrate pH 4.2, PEG 8000
|
Resolution 2.37 Å R-free 0.249 |
| 8OWV H6 and F2 nanobodies bound to SARS-CoV-2 spike RBD Deposited 2023-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain EEE
331–532（202 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000
|
Resolution 1.73 Å R-free 0.223 |
| 8OWW B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan) Deposited 2023-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
330–531（202 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 2 NO3 NITRATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Tris pH 8.5, PEG smear low
Seeded from crystals grown in ammonium nitrate, PEG 3350
|
Resolution 1.97 Å R-free 0.223 |
| 8OYT Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '3 up' RBD conformation Deposited 2023-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8OYU Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '2 up 1 down' RBD conformation Deposited 2023-05-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 8P5M SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab) Deposited 2023-05-24 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8P99 SARS-CoV-2 S-protein:D614G mutant in 1-up conformation Deposited 2023-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–681（667 aa）
Chain A
685–1213（529 aa）
Chain B
15–681（667 aa）
Chain B
685–1213（529 aa）
Chain C
15–681（667 aa）
Chain C
685–1213（529 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；HEPES pH 7.2 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8P9Y SARS-CoV-2 S protein S:D614G mutant in 3-down with binding site of an entry inhibitor Deposited 2023-06-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
15–681（667 aa）
Chain A
685–1213（529 aa）
Chain B
15–681（667 aa）
Chain B
685–1213（529 aa）
Chain C
15–681（667 aa）
Chain C
685–1213（529 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 NA SODIUM ION × 3 XIO [(2~{S})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{S})-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{H}-indol-3-yl]propanoyl]oxysodium × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；HEPES pH 7.2 150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 8PQ2 XBB 1.0 RBD bound to P4J15 (Local) Deposited 2023-07-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 8PSD SARS-CoV-2 XBB 1.0 closed conformation. Deposited 2023-07-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8Q5Y cryoEM structure of SARS-CoV2 Spike trimer in complex with Fab23 Deposited 2023-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain E
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 8Q7S Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01 Deposited 2023-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–526（193 aa）
|
Not recorded | P4G 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293.15 K；0.1 M Sodium Citrate pH 4.5
20% (w/v) PEG 4000
|
Resolution 2.70 Å R-free 0.283 |
| 8Q7S Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01 Deposited 2023-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
334–526（193 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293.15 K；0.1 M Sodium Citrate pH 4.5
20% (w/v) PEG 4000
|
Resolution 2.70 Å R-free 0.283 |
| 8Q7S Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01 Deposited 2023-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
334–526（193 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293.15 K；0.1 M Sodium Citrate pH 4.5
20% (w/v) PEG 4000
|
Resolution 2.70 Å R-free 0.283 |
| 8Q7S Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01 Deposited 2023-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293.15 K；0.1 M Sodium Citrate pH 4.5
20% (w/v) PEG 4000
|
Resolution 2.70 Å R-free 0.283 |
| 8Q7S Crystal structure of the SARS-CoV-2 RBD (Wuhan) with neutralizing VHHs Ma6F06 and Re21H01 Deposited 2023-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain M
334–526（193 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293.15 K；0.1 M Sodium Citrate pH 4.5
20% (w/v) PEG 4000
|
Resolution 2.70 Å R-free 0.283 |
| 8Q93 Crystal structure of the SARS-COV-2 RBD with neutralizing-VHHs Re30H02 and Re21D01 Deposited 2023-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–526（193 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；28% PEG smear broad, 50 mM arginine, 50 mM MSG, 5% Glycerol
|
Resolution 3.10 Å R-free 0.257 |
| 8Q94 Crystal structure of The SARS-COV-2 BA.2.75 RBD with neutralizing-VHHs Re32D03 and Ma3B12 Deposited 2023-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–517（184 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；293 K；0.1 M HEPES pH 7.0, 18% PEG 12000
|
Resolution 2.50 Å R-free 0.277 |
| 8Q95 Crystal structure of the SARS-CoV-2 BA.1 RBD with neutralizing-VHHs Ma16B06 and Ma3F05 Deposited 2023-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–517（184 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.8；293 K；0.1 M HEPES, 20% (v/v) PEG smear high, 0.15 M Lithium sulphate, 0.05 M magnesium chloride
|
Resolution 1.60 Å R-free 0.206 |
| 8QH0 Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194 Deposited 2023-09-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–528（198 aa）
|
Not recorded | PRO PROLINE × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；20% PEG 3350, 0.2 M lithium citrate
|
Resolution 1.87 Å R-free 0.209 |
| 8QPR SARS-CoV-2 S protein bound to human neutralising antibody UZGENT_G5 Deposited 2023-10-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8QQ0 SARS-CoV-2 S protein bound to neutralising antibody UZGENT_A3 Deposited 2023-10-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8QRF SARS-CoV-2 delta RBD complexed with XBB-6 and beta-49 Fabs Deposited 2023-10-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M citric acid pH 3.5 and 28% (w/v) PEG 8000
|
Resolution 3.70 Å R-free 0.317 |
| 8QRG SARS-CoV-2 delta RBD complexed with XBB-2 Fab and NbC1 Deposited 2023-10-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% (v/v) 1,4-Dioxane, 0.1 M Tris pH 8.0 and 15% (w/v) PEG 3350
|
Resolution 2.30 Å R-free 0.228 |
| 8QSQ Locally refined SARS-CoV-2 BA-2.86 Spike receptor binding domain (RBD) complexed with angiotensin converting enzyme 2 (ACE2) Deposited 2023-10-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–527（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8QTD Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab Deposited 2023-10-12 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8QZR SARS-CoV-2 delta RBD complexed with BA.4/5-9 Fab Deposited 2023-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-TRIS pH 6.5, 2% v/v Polyethylene glycol monomethyl ether 550, 1.8 M Ammonium sulfate
|
Resolution 3.77 Å R-free 0.300 |
| 8QZR SARS-CoV-2 delta RBD complexed with BA.4/5-9 Fab Deposited 2023-10-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-TRIS pH 6.5, 2% v/v Polyethylene glycol monomethyl ether 550, 1.8 M Ammonium sulfate
|
Resolution 3.77 Å R-free 0.300 |
| 8R1C SD1-2 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.20 Å |
| 8R1D SD1-3 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.37 Å |
| 8R80 SARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab nanobody Deposited 2023-11-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain R
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium acetate hydrate, 0.1 M sodium cacodylate pH 6.5, 40% PEG 300.
|
Resolution 4.03 Å R-free 0.313 |
| 8R80 SARS-CoV-2 Delta RBD in complex with XBB-9 Fab and an anti-Fab nanobody Deposited 2023-11-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium acetate hydrate, 0.1 M sodium cacodylate pH 6.5, 40% PEG 300.
|
Resolution 4.03 Å R-free 0.313 |
| 8R87 Cryo-EM structure of the Sars-Cov2 S trimer without RBDs Deposited 2023-11-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–331（331 aa）
Chain A
530–1208（679 aa）
Chain B
1–331（331 aa）
Chain B
530–1208（679 aa）
Chain C
1–331（331 aa）
Chain C
530–1208（679 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8R8K XBB-4 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein Deposited 2023-11-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1195（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 8RBU Crystal structure of HLA-A*11:01 in complex with SVLNDILARL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984) Deposited 2023-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
975–984（10 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 2 SO4 SULFATE ION × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.2M NaCl and 0.1M Tris HCl pH8.5
|
Resolution 2.70 Å R-free 0.252 |
| 8RBY The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.26 Deposited 2023-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MPO 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；40% PEG-5000 MME, 100mM MOPS pH 7, 10 mM CaCl2
|
Resolution 1.90 Å R-free 0.234 |
| 8RCV Crystal structure of HLA B*13:01 in complex with SVLNDIFSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984) Deposited 2023-12-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
975–984（10 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；14% PEG3350 and 0.1M NaFormate
|
Resolution 1.65 Å R-free 0.201 |
| 8REF Crystal structure of HLA B*13:01 in complex with SVLNDILARL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984) Deposited 2023-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
975–984（10 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 3 EDO 1,2-ETHANEDIOL × 4 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350 and 2% EG
|
Resolution 1.90 Å R-free 0.221 |
| 8RH6 Crystal structure of HLA-A*11:01 in complex with SVLNDILSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984) Deposited 2023-12-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain G
975–984（10 aa）
Chain H
975–984（10 aa）
Chain I
975–984（10 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.2M NaCl and 0.1M Tris HCl pH8.5
|
Resolution 3.32 Å R-free 0.251 |
| 8RHQ Crystal structure of HLA-A*11:01 in complex with SVLNDIFSRL, an 10-mer epitope from SARS-CoV-2 Spike (S975-984) Deposited 2023-12-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain G
975–984（10 aa）
Chain H
975–984（10 aa）
Chain I
975–984（10 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 17 NA SODIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1 CL CHLORIDE ION × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG3350, 0.2M Sodium acetate tihydrate pH 7.0
|
Resolution 2.00 Å R-free 0.244 |
| 8RJ5 P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；di-Sodium malonate, 0.1M
HEPES pH7, 0.1M
Poly(acrylic acid sodium salt) 2,100, 30% w/v
|
Resolution 3.02 Å R-free 0.260 |
| 8RJ5 P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain H
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；di-Sodium malonate, 0.1M
HEPES pH7, 0.1M
Poly(acrylic acid sodium salt) 2,100, 30% w/v
|
Resolution 3.02 Å R-free 0.260 |
| 8RJ7 The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG-3350, 100mM Bicine pH 9, 20 mM (NH4)2SO4
|
Resolution 2.10 Å R-free 0.222 |
| 8RJ7 The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 LYS LYSINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG-3350, 100mM Bicine pH 9, 20 mM (NH4)2SO4
|
Resolution 2.10 Å R-free 0.222 |
| 8RJ7 The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG-3350, 100mM Bicine pH 9, 20 mM (NH4)2SO4
|
Resolution 2.10 Å R-free 0.222 |
| 8RJ7 The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG-3350, 100mM Bicine pH 9, 20 mM (NH4)2SO4
|
Resolution 2.10 Å R-free 0.222 |
| 8RJ7 The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 1.29 Deposited 2023-12-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
332–528（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG-3350, 100mM Bicine pH 9, 20 mM (NH4)2SO4
|
Resolution 2.10 Å R-free 0.222 |
| 8RRN Crystal structure of the SARS-CoV-2 S RBD in complex with pT1616 Fab Deposited 2024-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；30% PEG 3000, 200 mM NaCl, 100 mM Tris pH 7.0
|
Resolution 3.11 Å R-free 0.291 |
| 8RRN Crystal structure of the SARS-CoV-2 S RBD in complex with pT1616 Fab Deposited 2024-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；30% PEG 3000, 200 mM NaCl, 100 mM Tris pH 7.0
|
Resolution 3.11 Å R-free 0.291 |
| 8S6M SARS-CoV-2 BQ.1.1 RBD bound to the S2V29 and the S2H97 Fab fragments Deposited 2024-02-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
328–531（204 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 9 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NI NICKEL (II) ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1 M Tris pH 8.5, 20% PEG-MME 2000, and 10 mM NiCl2
|
Resolution 1.67 Å R-free 0.203 |
| 8S9G SARS-CoV-2 BN.1 spike RBD bound to the human ACE2 ectodomain and the S309 neutralizing antibody Fab fragment Deposited 2023-03-28 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
328–529（202 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8SDF Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.4 Deposited 2023-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Z
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；65% MPD and 0.1 M Bicine pH 9.0
|
Resolution 1.79 Å R-free 0.218 |
| 8SDF Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.4 Deposited 2023-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；65% MPD and 0.1 M Bicine pH 9.0
|
Resolution 1.79 Å R-free 0.218 |
| 8SDG Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.43 Deposited 2023-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；1.0 M Li-chloride, 10% PEG-6000, and 0.1 M citric acid pH 4.0
|
Resolution 2.71 Å R-free 0.308 |
| 8SDG Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.43 Deposited 2023-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；1.0 M Li-chloride, 10% PEG-6000, and 0.1 M citric acid pH 4.0
|
Resolution 2.71 Å R-free 0.308 |
| 8SDH Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.56 Deposited 2023-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；10% ethylene glycol (v/v), 0.11 M MgCl2, and 16% polyethylene glycol 3350 (w/v)
|
Resolution 2.84 Å R-free 0.283 |
| 8SDH Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody CC25.56 Deposited 2023-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；10% ethylene glycol (v/v), 0.11 M MgCl2, and 16% polyethylene glycol 3350 (w/v)
|
Resolution 2.84 Å R-free 0.283 |
| 8SGU Crystal structure of the SARS-CoV-2 receptor binding domain Deposited 2023-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 FUC alpha-L-fucopyranose × 1 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% Jeffamine D2000, 10% Jeffamine M2005, 0.2 M NaCl, 0.1M MES pH 5.5
|
Resolution 1.95 Å R-free 0.199 |
| 8SIQ Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibodies CC25.36 and CV38-142 Fab Deposited 2023-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；273 K；20% (w/v) PEG-3350, 0.2 M di-Ammonium citrate
|
Resolution 2.50 Å R-free 0.287 |
| 8SIR Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC25.54 Fab Deposited 2023-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG 3350, 0.2 M potassium sodium tartrate, pH 7.2
|
Resolution 3.30 Å R-free 0.236 |
| 8SIS Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.2 Fab Deposited 2023-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3000, 0.1 M Sodium citrate pH 5.5
|
Resolution 3.08 Å R-free 0.303 |
| 8SIT Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.24 Fab Deposited 2023-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) PEG 3000, 0.1 M Sodium citrate pH 5.5
|
Resolution 2.91 Å R-free 0.309 |
| 8SIT Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.24 Fab Deposited 2023-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) PEG 3000, 0.1 M Sodium citrate pH 5.5
|
Resolution 2.91 Å R-free 0.309 |
| 8SIT Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.24 Fab Deposited 2023-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) PEG 3000, 0.1 M Sodium citrate pH 5.5
|
Resolution 2.91 Å R-free 0.309 |
| 8SIT Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with broadly neutralizing antibody CC84.24 Fab Deposited 2023-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% (w/v) PEG 3000, 0.1 M Sodium citrate pH 5.5
|
Resolution 2.91 Å R-free 0.309 |
| 8SK5 Crystal structure of the SARS-CoV-2 neutralizing VHH 7A9 bound to the spike receptor binding domain Deposited 2023-04-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2 M Sodium malonate pH 6.0, 18% PEG 3350
|
Resolution 2.01 Å R-free 0.211 |
| 8SMI Crystal structure of antibody WRAIR-2123 in complex with SARS-CoV-2 receptor binding domain Deposited 2023-04-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.12 M alcohol mixture (1,6-Hexanediol; 1-Butanol; 1,2-Propanediol; 2-Propanol; 1,4-Butanediol; 1,3-Propanediol),
0.1M buffer system 3 (Tris base and BICINE, pH 8.5),
50% precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350),
0.1 M Manganese(II) chloride tetrahydrate
|
Resolution 3.50 Å R-free 0.295 |
| 8SMT Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2023-04-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；8% v/v Tacsimate pH 5.0,
20% w/v Polyethylene glycol 3,350
|
Resolution 3.16 Å R-free 0.249 |
| 8SMT Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2023-04-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；8% v/v Tacsimate pH 5.0,
20% w/v Polyethylene glycol 3,350
|
Resolution 3.16 Å R-free 0.249 |
| 8SMT Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2023-04-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；8% v/v Tacsimate pH 5.0,
20% w/v Polyethylene glycol 3,350
|
Resolution 3.16 Å R-free 0.249 |
| 8SMT Crystal structure of antibody WRAIR-2134 in complex with SARS-CoV-2 receptor binding domain Deposited 2023-04-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
331–527（197 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；8% v/v Tacsimate pH 5.0,
20% w/v Polyethylene glycol 3,350
|
Resolution 3.16 Å R-free 0.249 |
| 8SUO BA.2/AZD1061/AZD3152 structure analysis Deposited 2023-05-12 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–527（195 aa）
Fragment：receptor-binding domain (UNP residues 333-527)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M D-glucose, 0.12 M D-mannose, 0.12 M D-galactose, 0.12 M L-fructose, 0.12 M D-xylose, 0.12 M N-acetyl-D-glucosamine, 0.1 M Tris, 0.1 M bicine, pH 8.5, 40% v/v ethylene glycol, 20% w/v PEG8000
|
Resolution 3.30 Å R-free 0.332 |
| 8SWH Local refinement of SARS-CoV-2 (HP-GSAS-Mut7) spike NTD in complex with TXG-0078 Fab Deposited 2023-05-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；1X TBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.88 Å |
| 8T20 Cryo-EM structure of mink variant Y453F trimeric spike protein bound to two mink ACE2 receptors Deposited 2023-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM Tris pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 8T22 Cryo-EM structure of mink variant Y453F trimeric spike protein bound to one mink ACE2 receptors at downRBD conformation Deposited 2023-06-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.83 Å |
| 8T23 Cryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement at upRBD conformation Deposited 2023-06-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
321–528（208 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM Tris pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.87 Å |
| 8T25 Cryo-EM structure of the RBD-ACE2 interface of the SARS-CoV-2 trimeric spike protein bound to ACE2 receptor after local refinement at downRBD conformation. Deposited 2023-06-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
321–528（208 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |
| 8TAZ Cryo-EM structure of mink variant Y453F trimeric spike protein bound to one mink ACE2 receptors Deposited 2023-06-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM Tris pH 8.0, 200 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å |
| 8THF SARS-CoV-2 BA.1 S-6P-no-RBD Deposited 2023-07-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–327（314 aa）
Fragment：RBD truncated,RBD truncated
Chain A
525–1211（687 aa）
Fragment：RBD truncated,RBD truncated
Chain B
14–327（314 aa）
Fragment：RBD truncated,RBD truncated
Chain B
525–1211（687 aa）
Fragment：RBD truncated,RBD truncated
Chain C
14–327（314 aa）
Fragment：RBD truncated,RBD truncated
Chain C
525–1211（687 aa）
Fragment：RBD truncated,RBD truncated
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 8TM1 Antibody N3-1 bound to RBDs in the up and down conformations Deposited 2023-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
|
Mutation：Hexapro construct Mutation：Hexapro construct | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris pH 8.0, 200 mM NaCl, 0.02% NaN3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 8TMA Antibody N3-1 bound to RBD in the up conformation Deposited 2023-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：Hexapro construct | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；2 mM Tris pH 8.0, 200 mM NaCl, 0.02% NaN3
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8TMY Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CHM-16 Deposited 2023-07-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain M
1140–1164（25 aa）
|
Not recorded | FLC CITRATE ANION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium cacodylate pH 6.5, and 1 M sodium citrate
|
Resolution 3.07 Å R-free 0.286 |
| 8TMY Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CHM-16 Deposited 2023-07-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain N
1140–1164（25 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium cacodylate pH 6.5, and 1 M sodium citrate
|
Resolution 3.07 Å R-free 0.286 |
| 8TMY Crystal structure of SARS-CoV-2 spike stem helix peptide in complex with neutralizing antibody CHM-16 Deposited 2023-07-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain S
1140–1164（25 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium cacodylate pH 6.5, and 1 M sodium citrate
|
Resolution 3.07 Å R-free 0.286 |
| 8TYL Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2 Deposited 2023-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 8TYO Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2 Deposited 2023-08-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
19–1211（1193 aa）
Chain B
19–1211（1193 aa）
Chain C
19–1211（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 8U1G Prefusion-stabilized SARS-CoV-2 S2 subunit Deposited 2023-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
697–1141（445 aa）
|
Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 8% (v/v) ethylene glycol and 10% (v/v) PEG 8000
|
Resolution 3.20 Å R-free 0.262 |
| 8U1G Prefusion-stabilized SARS-CoV-2 S2 subunit Deposited 2023-08-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain B
697–1141（445 aa）
|
Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5, 8% (v/v) ethylene glycol and 10% (v/v) PEG 8000
|
Resolution 3.20 Å R-free 0.262 |
| 8U28 Gaussian mixture model based single particle refinement - SARS (SARS-CoV-2 Spike Proteins on intact virions from EMPIAR-10492) Deposited 2023-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8UG9 XBB.1.5 spike/Nb5 complex Deposited 2023-10-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 8UIR SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.16) Deposited 2023-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：residues 682-685 mutated from RRAR to GSAS Mutation：residues 682-685 mutated from RRAR to GSAS Mutation：residues 682-685 mutated from RRAR to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8UK1 SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer consensus (S-RRAR-Omicron-XBB.1.16) Deposited 2023-10-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8UKD SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-XBB.1.5) Deposited 2023-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8UKF SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer consensus (S-GSAS-Omicron-EG.5) Deposited 2023-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8USZ Cryo-EM Structure of Full-Length Spike Protein of Omicron XBB.1.5 Deposited 2023-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1273（1258 aa）
Chain B
16–1273（1258 aa）
Chain C
16–1273（1258 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；25mM Tris (pH 7.5), 150mM NaCl, 1.0mM EDTA, 0.02% DDM
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 8UUL Prototypic SARS-CoV-2 spike (containing K417) in the closed conformation Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8UUM Prototypic SARS-CoV-2 spike (containing K417) in the open conformation Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | MAN alpha-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8UUN Prototypic SARS-CoV-2 spike (containing V417) in the closed conformation Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 8UUO Prototypic SARS-CoV-2 spike (containing V417) in the open conformation Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1211（1211 aa）
Chain B
1–1211（1211 aa）
Chain C
1–1211（1211 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 MAN alpha-D-mannopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8V0L SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer 1 (S-RRAR-Omicron-XBB.1.16) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8V0M SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer 2 (S-RRAR-Omicron-XBB.1.16) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8V0N SARS-CoV-2 Omicron-XBB.1.16 3-RBD-down Spike Protein Trimer 3 (S-RRAR-Omicron-XBB.1.16) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8V0O SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-XBB.1.16) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8V0P SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.16) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8V0Q SARS-CoV-2 Omicron-XBB.1.16 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-XBB.1.16) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8V0R SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-XBB.1.5) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8V0S SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-XBB.1.5) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8V0T SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-XBB.1.5) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8V0U SARS-CoV-2 Omicron-XBB.1.5 3-RBD down Spike Protein Trimer 4 (S-GSAS-Omicron-XBB.1.5) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8V0V SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8V0W SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8V0X SARS-CoV-2 Omicron-EG.5 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-EG.5) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8V4F Model and map from local refinement of a CAB-A17 - Omicron Ba.1 spike complex Deposited 2023-11-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–526（193 aa）
Fragment：Omicron BA.1 RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.68 Å |
| 8V5V Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation Deposited 2023-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain E
691–1211（521 aa）
Chain F
691–1211（521 aa）
Chain G
691–1211（521 aa）
|
Mutation：F817P,A892P,A899P,A942P,V987P,Y707C,T883C,Y788C,A876C Mutation：F817P,A892P,A899P,A942P,V987P,Y707C,T883C,Y788C,A876C Mutation：F817P,A892P,A899P,A942P,V987P,Y707C,T883C,Y788C,A876C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；Filtered and degased
cryo-EM vitrification conditions
Cryogen ETHANE；6 seconds blotting time at force 0
|
Resolution 2.93 Å |
| 8VAO Simulation-driven design of prefusion stabilized SARS-CoV-2 spike S2 antigen Deposited 2023-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
697–1208（512 aa）
Chain B
697–1208（512 aa）
Chain C
697–1208（512 aa）
|
Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P, V991W, T998W Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P, V991W, T998W Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P, V991W, T998W | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8VCR SARS-CoV-2 Spike S2 bound to Fab 54043-5 Deposited 2023-12-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
697–1208（512 aa）
Chain B
697–1208（512 aa）
Chain C
697–1208（512 aa）
|
Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P Mutation：S704C, K790C, F817P, A892P, A899P, A942P, Q957E, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8VIA Protective effect of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination Deposited 2024-01-03 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
677–1208（532 aa）
Chain D
15–676（662 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8VIF SARS-CoV-2 spike omicron (BA.1) ectodomain trimer in complex with SC27 Fab, local refinement Deposited 2024-01-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
1–1208（1208 aa）
|
Mutation：pre-fusion stabilized: F817P, A892P, A899P, A942P, K986P, V987P, 682-685 RRAR mutated to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VKE SARS-CoV-2 spike omicron (BA.1) RBD ectodomain dimer-of-trimers in complex with SC27 Fabs Deposited 2024-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain C
1–1208（1208 aa）
Chain R
1–1208（1208 aa）
|
Mutation：pre-fusion stabilized: F817P, A892P, A899P, A942P, K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：pre-fusion stabilized: F817P, A892P, A899P, A942P, K986P, V987P, 682-685 RRAR mutated to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8VKK Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein Deposited 2024-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.81 Å |
| 8VKL Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (conformation 2) Deposited 2024-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.91 Å |
| 8VKM Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (conformation 1) Deposited 2024-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 8VKN Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with mouse ACE2 (focused refinement of RBD and mouse ACE2) Deposited 2024-01-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
327–527（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 8VKO Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 Deposited 2024-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.68 Å |
| 8VKP Cryo-EM structure of SARS-CoV-2 XBB.1.5 spike protein in complex with human ACE2 (focused refinement of RBD and ACE2) Deposited 2024-01-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
327–527（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 8VQ9 Prefusion stabilized structure of the SARS-CoV-2 fusion machinery Deposited 2024-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
686–1208（523 aa）
Chain B
686–1208（523 aa）
Chain C
686–1208（523 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8VQA Prefusion stabilized structure of the SARS-CoV-2 fusion machinery Deposited 2024-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
686–1208（523 aa）
Chain B
686–1208（523 aa）
Chain C
686–1208（523 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 8VQB Prefusion stabilized structure of the SARS-CoV-2 fusion machinery Deposited 2024-01-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
686–1208（523 aa）
Chain B
686–1208（523 aa）
Chain C
686–1208（523 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8VQR Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric raccoon dog ACE2 Deposited 2024-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–536（218 aa）
Fragment：receptor-binding domain
|
Mutation：;Q321V, T323S, E324G, S325D, I326V, A348P, N354E, R357K, A372T, S373F, P384A, T393S, I402V, R403K, E406D, K417V, T430M, I434L, S438T, N439R, L441I, S443A, V445S, G446T, L452K, H519N, K529L, N532D, V534I, N536S ; | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Tris (pH 8-8.5), 18-22% PEG 6000, 100 mM NaCl and ethylene glycol (0.5-2%)
|
Resolution 2.56 Å R-free 0.264 |
| 8VQR Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric raccoon dog ACE2 Deposited 2024-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
319–536（218 aa）
Fragment：receptor-binding domain
|
Mutation：;Q321V, T323S, E324G, S325D, I326V, A348P, N354E, R357K, A372T, S373F, P384A, T393S, I402V, R403K, E406D, K417V, T430M, I434L, S438T, N439R, L441I, S443A, V445S, G446T, L452K, H519N, K529L, N532D, V534I, N536S ; | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Tris (pH 8-8.5), 18-22% PEG 6000, 100 mM NaCl and ethylene glycol (0.5-2%)
|
Resolution 2.56 Å R-free 0.264 |
| 8VYA SARS-CoV-2 Omicron Variant Spike Glycoprotein Fusion Core (Q954H) Deposited 2024-02-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
912–966（55 aa）
Chain B
912–966（55 aa）
Chain C
912–966（55 aa）
Chain D
1168–1203（36 aa）
Chain E
1168–1203（36 aa）
Chain F
1168–1203（36 aa）
|
Mutation：Q954H Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Q954H Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：Q954H Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；20 mM 1,6-hexanediol; 20 mM 1 butanol; 20 mM 1,2-propanediol; 20 mM 2-propanol; 20 mM 1,4-butanediol; 20 mM 1,3-propanediol; 12.5% PEG1000; 12.5% PEG3350; 12.5% 2-methyl-2,4-pentanediol; 100 mM imidazole/MES monohydrate buffer (pH 6.5)
|
Resolution 2.12 Å R-free 0.250 |
| 8VYE SARS-CoV-2 S (C.37 Lambda variant) plus S309, S2L20, and S2X303 Fabs Deposited 2024-02-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric |
Chain E
1–1208（1208 aa）
Chain K
1–1208（1208 aa）
Chain O
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 57 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8VYF SARS-CoV-2 S NTD (C.37 Lambda variant) plus S2L20 and S2X303 Fabs, local refinement Deposited 2024-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8VYG SARS-CoV-2 S RBD (C.37 Lambda variant) plus S309 Fab, local refinement Deposited 2024-02-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8W4F SARS-CoV-2 spike protein in complex with a trivalent nanobody Deposited 2023-08-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
27–1146（1120 aa）
Chain B
27–1146（1120 aa）
Chain C
27–1146（1120 aa）
|
Mutation：R683A/R685A/F817P/A892P/A899P/A942P/R986P/V987P Mutation：R683A/R685A/F817P/A892P/A899P/A942P/R986P/V987P Mutation：R683A/R685A/F817P/A892P/A899P/A942P/R986P/V987P | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；20 mM Tris,150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 8WDR Crystal structure of BQ.1.1 RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate 5.5, 15% w/v PEG 6000 (MD1-38-1-43)
|
Resolution 3.47 Å R-free 0.269 |
| 8WDR Crystal structure of BQ.1.1 RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Sodium citrate 5.5, 15% w/v PEG 6000 (MD1-38-1-43)
|
Resolution 3.47 Å R-free 0.269 |
| 8WDS Crystal structure of BF.7 RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 0.1 M Tris pH 8.0, 20% w/v PEG 6000 (MD1-29-1-43)
|
Resolution 3.40 Å R-free 0.271 |
| 8WDS Crystal structure of BF.7 RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium chloride, 0.1 M Tris pH 8.0, 20% w/v PEG 6000 (MD1-29-1-43)
|
Resolution 3.40 Å R-free 0.271 |
| 8WDY SARS-CoV-2 Omicron BQ.1.1 RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.69 Å |
| 8WDZ SARS-CoV-2 Omicron BQ.1 RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–540（222 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.71 Å |
| 8WE0 SARS-CoV-2 Omicron XBB RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 8WE1 SARS-CoV-2 Omicron BF.7 RBD complexed with human ACE2 Deposited 2023-09-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.47 Å |
| 8WE4 SARS-CoV-2 Omicron XBB.1.5 RBD complexed with human ACE2 and S304 Deposited 2023-09-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
319–541（223 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.91 Å |
| 8WFH Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1 Deposited 2023-09-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: trimeric |
Chain A
333–530（198 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；25% w/v PEG 1500, SPG Buffer/NaOH pH 8.5
|
Resolution 2.72 Å R-free 0.250 |
| 8WFM Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11 Deposited 2023-09-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.05M Citric acid,0.05M BIS-TRIS propane/PH5.0,16%Polyethylene glycol 3350
|
Resolution 2.99 Å R-free 0.265 |
| 8WFM Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11 Deposited 2023-09-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.05M Citric acid,0.05M BIS-TRIS propane/PH5.0,16%Polyethylene glycol 3350
|
Resolution 2.99 Å R-free 0.265 |
| 8WFM Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11 Deposited 2023-09-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.05M Citric acid,0.05M BIS-TRIS propane/PH5.0,16%Polyethylene glycol 3350
|
Resolution 2.99 Å R-free 0.265 |
| 8WFM Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11 Deposited 2023-09-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain H
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.05M Citric acid,0.05M BIS-TRIS propane/PH5.0,16%Polyethylene glycol 3350
|
Resolution 2.99 Å R-free 0.265 |
| 8WGV BA.2(S375) Spike (S6P)/hACE2 complex Deposited 2023-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.92 Å |
| 8WGW Local refinement of RBD-ACE2 Deposited 2023-09-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–1208（1208 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8WHS Spike Trimer of BA.2.86 in complex with one hACE2 Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 8WHU Spike Trimer of BA.2.86 in complex with two hACE2s Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 41 ZN ZINC ION × 2 CL CHLORIDE ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8WHV Spike Trimer of BA.2.86 with three RBDs down Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 8WHW Spike Trimer of BA.2.86 with single RBD up Deposited 2023-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 8WHZ BA.2.86 RBD in complex with hACE2 (local refinement) Deposited 2023-09-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.93 Å |
| 8WLO Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with hippopotamus ACE2 Deposited 2023-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1217（1217 aa）
Chain B
1–1217（1217 aa）
Chain C
1–1217（1217 aa）
|
Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.62 Å |
| 8WLR Cryo-EM structure of SARS-CoV-2 prototype spike protein receptor-binding domain in complex with hippopotamus ACE2 Deposited 2023-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1217（1217 aa）
Fragment：receptor-binding domain
|
Mutation：R682G,R683S,R685S,F817P,A892P,A899P,A942P,K986P,V987P | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.12 Å |
| 8WMD Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-2 state) Deposited 2023-10-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: monomeric |
Chain A
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.71 Å |
| 8WMF Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein (closed-1 state) Deposited 2023-10-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 5 PDB declaration: trimeric |
Chain A
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.51 Å |
| 8WOX Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with rabbit ACE2 (local refinement) Deposited 2023-10-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
| 8WOY Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with rabbit ACE2 (local refinement) Deposited 2023-10-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–539（221 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.14 Å |
| 8WP8 Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 Deposited 2023-10-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.89 Å |
| 8WPW Cryo-EM structure of SARS-CoV-2 XBB.1.5 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies Deposited 2023-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain R
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.49 Å |
| 8WPY Cryo-EM structure of SARS-CoV-2 receptor-binding domain (RBD) complexed with CB6 mutant,S309, and S304 antibodies Deposited 2023-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain R
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.02 Å |
| 8WRH SARS-CoV-2 XBB.1.5.70 in complex with ACE2 Deposited 2023-10-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–529（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å |
| 8WRL XBB.1.5 RBD in complex with ACE2 Deposited 2023-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–537（219 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.36 Å |
| 8WRM XBB.1.5 spike protein in complex with ACE2 Deposited 2023-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
1–1140（1140 aa）
Chain F
1–1140（1140 aa）
Chain G
1–1140（1140 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.34 Å |
| 8WRO XBB.1.5.10 spike protein in complex with ACE2 Deposited 2023-10-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8WTD XBB.1.5.10 RBD in complex with ACE2 Deposited 2023-10-18 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–534（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 8WTJ XBB.1.5.70 spike protein in complex with ACE2 Deposited 2023-10-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.64 Å |
| 8WXL Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state) Deposited 2023-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.59 Å |
| 8WYH The global map of Omicron Subvariants Spike with ACE2 Deposited 2023-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
17–1147（1131 aa）
Chain B
17–1147（1131 aa）
Chain C
17–1147（1131 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 8WYJ The global map of Omicron Subvariants Spike with two antibodies Deposited 2023-10-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: 15-meric |
Chain A
17–1147（1131 aa）
Chain B
17–1147（1131 aa）
Chain C
17–1147（1131 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 8WZI One RBD up state of Spike glycoprotein, SARS-CoV-2 Deposited 2023-11-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：(RRAR)682A,K986P, V987P Mutation：(RRAR)682A,K986P, V987P Mutation：(RRAR)682A,K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；Blot force, 0
|
Resolution 3.00 Å |
| 8X0X Crystal structure of JE-5C in complex with SARS-CoV-2 RBD Deposited 2023-11-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
334–528（195 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M magnesium sulfate heptahydrate
20 % (w/v) polyethylene glycol 3350
|
Resolution 3.45 Å R-free 0.285 |
| 8X0X Crystal structure of JE-5C in complex with SARS-CoV-2 RBD Deposited 2023-11-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
334–528（195 aa）
Fragment：receptor-binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M magnesium sulfate heptahydrate
20 % (w/v) polyethylene glycol 3350
|
Resolution 3.45 Å R-free 0.285 |
| 8X0Y Crystal structure of JM-1A in complex with SARS-CoV-2 RBD Deposited 2023-11-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–528（196 aa）
|
Not recorded | CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；1M lithium chloride, 0.1M citrate pH 4.0, 20% (w/v) polyethylene glycol 6000
|
Resolution 1.94 Å R-free 0.223 |
| 8X0Y Crystal structure of JM-1A in complex with SARS-CoV-2 RBD Deposited 2023-11-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；1M lithium chloride, 0.1M citrate pH 4.0, 20% (w/v) polyethylene glycol 6000
|
Resolution 1.94 Å R-free 0.223 |
| 8X4H SARS-CoV-2 JN.1 Spike Deposited 2023-11-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.65 Å |
| 8X4Z BA.2.86 Spike Trimer with ins483V mutation (3 RBD down) Deposited 2023-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.49 Å |
| 8X50 BA.2.86 Spike Trimer with ins483V mutation (1 RBD up) Deposited 2023-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.82 Å |
| 8X55 BA.2.86 Spike Trimer with T356K mutation (3 RBD down) Deposited 2023-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å |
| 8X56 BA.2.86 Spike Trimer with T356K mutation (1 RBD up) Deposited 2023-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.93 Å |
| 8X5Q SARS-CoV-2 BA.2.75 Spike with K356T mutation (3 RBD down) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K356T Mutation：K356T Mutation：K356T | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 8X5R SARS-CoV-2 BA.2.75 Spike with K356T mutation (1 RBD up) Deposited 2023-11-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：K356T Mutation：K356T Mutation：K356T | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.72 Å |
| 8XAL Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with ACE2 Deposited 2023-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：;T19I, L24S, 25-27del, 69-70del, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, R682G, R683S, R685S, N764K, D796Y, F817P, N856K, A892P, A899P, A942P, Q954H, N969K, K986, V987P ; Mutation：;T19I, L24S, 25-27del, 69-70del, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, R682G, R683S, R685S, N764K, D796Y, F817P, N856K, A892P, A899P, A942P, Q954H, N969K, K986, V987P ; Mutation：;T19I, L24S, 25-27del, 69-70del, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, R682G, R683S, R685S, N764K, D796Y, F817P, N856K, A892P, A899P, A942P, Q954H, N969K, K986, V987P ; | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
|
Resolution 3.20 Å |
| 8XBF Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with antibody O5C2 Deposited 2023-12-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：;T19I, L24S, 25-27del, 69-70del, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, R682G, R683S, R685S, N764K, D796Y, F817P, N856K, A892P, A899P, A942P, Q954H, N969K, K986, V987P ; Mutation：;T19I, L24S, 25-27del, 69-70del, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, R682G, R683S, R685S, N764K, D796Y, F817P, N856K, A892P, A899P, A942P, Q954H, N969K, K986, V987P ; Mutation：;T19I, L24S, 25-27del, 69-70del, G142D, V213G, G339D, S371F, S373P, S375F, T376A, D405N, R408S, K417N, N440K, K444T, L452R, N460K, S477N, T478K, E484A, F486V, Q498R, N501Y, Y505H, D614G, H655Y, N679K, P681H, R682G, R683S, R685S, N764K, D796Y, F817P, N856K, A892P, A899P, A942P, Q954H, N969K, K986, V987P ; | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
|
Resolution 3.60 Å |
| 8XE9 XBB.1.5 RBD in complex with BD55-1205 Deposited 2023-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
334–529（196 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8XEA XBB.1.5 spike protein in complex with BD55-1205 Deposited 2023-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain D
1–1140（1140 aa）
Chain E
1–1140（1140 aa）
Chain F
1–1140（1140 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 8XEF Cocktail GC2050-GC2225 Deposited 2023-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
334–528（195 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.41 Å |
| 8XG2 The structure of HLA-A/Pep14 Deposited 2023-12-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
340–351（12 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1M Bis-Tris, 20%w/v Polyethylene glycol monomethyl ether 5000
|
Resolution 1.84 Å R-free 0.230 |
| 8XI6 SARS-CoV-2 Omicron BQ.1.1 Variant Spike Protein Complexed with MO11 Fab Deposited 2023-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 8XK2 A neutralizing nanobody VHH60 against wt SARS-CoV-2 Deposited 2023-12-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–531（213 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；1.0 M Sodium acetate trihydrate, 0.1 M Sodium HEPES 7.5
|
Resolution 3.40 Å R-free 0.300 |
| 8XK2 A neutralizing nanobody VHH60 against wt SARS-CoV-2 Deposited 2023-12-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
319–531（213 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；1.0 M Sodium acetate trihydrate, 0.1 M Sodium HEPES 7.5
|
Resolution 3.40 Å R-free 0.300 |
| 8XK2 A neutralizing nanobody VHH60 against wt SARS-CoV-2 Deposited 2023-12-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–531（213 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；1.0 M Sodium acetate trihydrate, 0.1 M Sodium HEPES 7.5
|
Resolution 3.40 Å R-free 0.300 |
| 8XK2 A neutralizing nanobody VHH60 against wt SARS-CoV-2 Deposited 2023-12-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
319–531（213 aa）
Fragment：receptor binding domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；1.0 M Sodium acetate trihydrate, 0.1 M Sodium HEPES 7.5
|
Resolution 3.40 Å R-free 0.300 |
| 8XKC The structure of HLA-A/Pep16 Deposited 2023-12-23 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
361–369（9 aa）
Fragment：Pep16
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1M Imidazole, 20%w/v PEG 6000
|
Resolution 2.18 Å R-free 0.291 |
| 8XKI A neutralizing nanobody VHH60 against wt SARS-CoV-2 Deposited 2023-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8XLM Structure of the SARS-CoV-2 EG.5.1 spike glycoprotein in complex with ACE2 (1-up state) Deposited 2023-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.22 Å |
| 8XLN Structure of the SARS-CoV-2 EG.5.1 spike RBD in complex with ACE2 Deposited 2023-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；calcium- and magnesium-free PBS buffer.
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.78 Å |
| 8XLV Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P), 1-RBD-up state Deposited 2023-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1147（1120 aa）
Chain B
28–1147（1120 aa）
Chain C
28–1147（1120 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 8XM5 Cryo-EM structure of SARS-CoV-2 Omicron EG.5 spike protein(6P), RBD-closed state Deposited 2023-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.61 Å |
| 8XMG Cryo-EM structure of SARS-CoV-2 Omicron HV.1 spike protein(6P), RBD-closed state Deposited 2023-12-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1208（1181 aa）
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 8XMT Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P), RBD-closed state Deposited 2023-12-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1207（1192 aa）
Chain B
16–1207（1192 aa）
Chain C
16–1207（1192 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.31 Å |
| 8XN2 SARS-CoV-2 Omicron EG.5.1 RBD in complex with human ACE2 (local refined from the spike protein) Deposited 2023-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.79 Å |
| 8XN3 SARS-CoV-2 Omicron HV.1 RBD in complex with human ACE2 (local refinement from the spike protein) Deposited 2023-12-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8XN5 Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2 Deposited 2023-12-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
16–1207（1192 aa）
Chain C
16–1207（1192 aa）
Chain D
16–1207（1192 aa）
|
Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.87 Å |
| 8XNF Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 spike protein(6P) in complex with human ACE2 Deposited 2023-12-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
28–1147（1120 aa）
Chain C
28–1147（1120 aa）
Chain D
28–1147（1120 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.26 Å |
| 8XNK Cryo-EM structure of SARS-CoV-2 Omicron HV.1 spike protein(6P) in complex with human ACE2 Deposited 2023-12-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
28–1208（1181 aa）
Chain C
28–1208（1181 aa）
Chain D
28–1208（1181 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.78 Å |
| 8XRQ SARS-CoV-2 BA.1 spike RBD in complex bound with VacBB-639 Deposited 2024-01-08 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；blot for 5s, wait for 2s, blot force:0
|
Resolution 4.19 Å |
| 8XSD BA.5 Spike complex with CR9 Deposited 2024-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 8XSE SARS-CoV-2 RBD + IMCAS-123 + IMCAS-72 Fab Deposited 2024-01-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
319–527（209 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 8XSF SARS-CoV-2 RBD + IMCAS-364 + hACE2 Deposited 2024-01-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
319–527（209 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.16 Å |
| 8XSI SARS-CoV-2 RBD + IMCAS-364 (Local Refinement) Deposited 2024-01-09 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
319–527（209 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.10 Å |
| 8XSJ SARS-CoV-2 Omicron BA.4 RBD + IMCAS-316 + ACE2 Deposited 2024-01-09 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
319–541（223 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.61 Å |
| 8XSL SARS-CoV-2 spike + IMCAS-123 Deposited 2024-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8XUR BA.2.86 Spike Trimer in complex with heparan sulfate Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 34 IDU 2-O-sulfo-beta-L-altropyranuronic acid × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 8XUS JN.1 Spike Trimer in complex with heparan sulfate Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 54 IDU 2-O-sulfo-beta-L-altropyranuronic acid × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 8XUT XBB.1.5 Spike Trimer in complex with heparan sulfate Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 IDU 2-O-sulfo-beta-L-altropyranuronic acid × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 8XUU BA.2.86-T356K Spike Trimer in complex with heparan sulfate (Local refinement) Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–1208（1208 aa）
|
Mutation：T356K | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 IDU 2-O-sulfo-beta-L-altropyranuronic acid × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 8XUX Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state) Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1210（1183 aa）
Chain B
28–1210（1183 aa）
Chain C
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.22 Å |
| 8XUY Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up state) Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
28–1210（1183 aa）
Chain B
28–1210（1183 aa）
Chain C
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.14 Å |
| 8XUZ Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (2-up and 1-down state) Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
28–1210（1183 aa）
Chain B
28–1210（1183 aa）
Chain C
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.05 Å |
| 8XV0 Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state) Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.00 Å |
| 8XV1 Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (down state) Deposited 2024-01-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.05 Å |
| 8XVM Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state) Deposited 2024-01-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: dimeric |
Chain A
28–1210（1183 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 2.77 Å |
| 8XXW Fab M2-7 complexed with SARS-Cov2 RBD and human ACE2 Deposited 2024-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
336–515（180 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 8XY9 Crystal structure of SARS-CoV-2 BF.7 RBD and human ACE2 complex Deposited 2024-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES, pH 7.0,10%w/v Polyethylene glycol 6000.
|
Resolution 3.64 Å R-free 0.261 |
| 8XY9 Crystal structure of SARS-CoV-2 BF.7 RBD and human ACE2 complex Deposited 2024-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–526（194 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1 M HEPES, pH 7.0,10%w/v Polyethylene glycol 6000.
|
Resolution 3.64 Å R-free 0.261 |
| 8XYE Crystal structure of SARS-CoV-2 BA.4 RBD and human ACE2 Deposited 2024-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–526（194 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1M BICINE, pH9.0,10% w/v PEG20000,2% v/v 1,4-Dioxane
|
Resolution 3.32 Å R-free 0.242 |
| 8XYE Crystal structure of SARS-CoV-2 BA.4 RBD and human ACE2 Deposited 2024-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–526（194 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1M BICINE, pH9.0,10% w/v PEG20000,2% v/v 1,4-Dioxane
|
Resolution 3.32 Å R-free 0.242 |
| 8XYG Crystal structure of SARS-CoV-2 BQ.1.1 RBD and human ACE2 Deposited 2024-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–525（192 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M BIS-TRIS, pH6.5, 16% w/v PEG10000
|
Resolution 3.64 Å R-free 0.291 |
| 8XYG Crystal structure of SARS-CoV-2 BQ.1.1 RBD and human ACE2 Deposited 2024-01-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
334–525（192 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M BIS-TRIS, pH6.5, 16% w/v PEG10000
|
Resolution 3.64 Å R-free 0.291 |
| 8XYH Cryo-EM structure of BANAL-20-52 spike protein (6P) Deposited 2024-01-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1217（1217 aa）
Chain B
1–1217（1217 aa）
Chain C
1–1217（1217 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 8XYM Cryo-EM structure of CX1 spike protein (6P) Deposited 2024-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1214（1214 aa）
Chain B
1–1214（1214 aa）
Chain C
1–1214（1214 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.74 Å |
| 8XYO Cryo-EM structure of CX1 receptor binding domain in complex with human ACE2 Deposited 2024-01-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1214（1214 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8XYZ The structure of fox ACE2 and PT RBD complex Deposited 2024-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
323–541（219 aa）
Fragment：RBD
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 8XZ0 Crystal complex structure of SARS-CoV-2 S bound to human ezrin Deposited 2024-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1260–1273（14 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.4；289 K；0.22 M Magnesium acetate and 19% PEG 3350,
|
Resolution 2.04 Å R-free 0.253 |
| 8XZ4 SARS-CoV-2 S and radixin complex structure Deposited 2024-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1260–1273（14 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；75 mM Sodium acetate, 0.1 M Tris-HCl, pH 7.4, 5.5% PEG 3350
|
Resolution 2.13 Å R-free 0.266 |
| 8XZ5 SARS-CoV-2 S and moesin complex structure Deposited 2024-01-20 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1260–1273（14 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.1 M Tris, pH 7.4, 0.2 M NH4Ac, and 21% PEG 3350
|
Resolution 1.80 Å R-free 0.232 |
| 8XZ8 BA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2) Deposited 2024-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Not recorded | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.65 Å |
| 8XZ9 BA.2.86 Spike in complex with bovine ACE2 (bound 2 ACE2) Deposited 2024-01-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
28–1144（1117 aa）
Chain C
28–1144（1117 aa）
Chain D
28–1144（1117 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 8XZA BA.2.86 Spike in complex with bovine ACE2 (Local refinement) Deposited 2024-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.07 Å |
| 8XZD The structure of fox ACE2 and Omicron BF.7 RBD complex Deposited 2024-01-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：RBD
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 8Y0Y Cryo-EM structure of the 123-316 scDb/PT-RBD complex Deposited 2024-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–527（209 aa）
Fragment：Receptor binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.86 Å |
| 8Y16 Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein in complex with human ACE2 Deposited 2024-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | ZN ZINC ION × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 8Y18 Cryo-EM structure of SARS-CoV-2 Omicron JN.1 RBD in complex with human ACE2 (local refinement from the spike protein) Deposited 2024-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8Y4A BA.2.86 S-trimer in complex with Nab XG2v046 Deposited 2024-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8Y4C BA.2.86 S-trimer in complex with Nab XGv280 Deposited 2024-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 54 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.75 Å |
| 8Y5J Cryo-EM structure of SARS-CoV-2 Omicron JN.1 spike protein Deposited 2024-01-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 8Y6A Cryo-EM structure of SARS-CoV-2 Omicron BA.2.86 RBD in complex with human ACE2 and S309 Fab Deposited 2024-02-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
319–541（223 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å |
| 8YBS State - I: Spike 2-up RBD with THSC20.HVTR04 (Fab4) Deposited 2024-02-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain B
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 35 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.54 Å |
| 8YBY State - I: Spike 2-up RBD with THSC20.HVTR26 (Fab26) - single Fab masked Deposited 2024-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain B
1–1273（1273 aa）
Chain D
1–1273（1273 aa）
Chain E
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 8YBZ State - II: Spike 3-up RBD with THSC20.HVTR26 (Fab26) Deposited 2024-02-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 8YDP Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9 Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES (pH 7.5), 10% PEG 8000
|
Resolution 2.30 Å R-free 0.263 |
| 8YDP Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9 Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES (pH 7.5), 10% PEG 8000
|
Resolution 2.30 Å R-free 0.263 |
| 8YDQ Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with Ce149 Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium thiocyanate, 20% PEG 6000
|
Resolution 1.90 Å R-free 0.249 |
| 8YDR Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce59 Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.08 M MES (pH 6.5), 0.16 M calcium acetate hydrate, 14.4% PEG 8000, 20% glycerol
|
Resolution 2.30 Å R-free 0.266 |
| 8YDS Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59 Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M BICINE (pH 9.0), 20% PEG 6000
|
Resolution 1.90 Å R-free 0.226 |
| 8YDT Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41 Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium formate dihydrate
|
Resolution 2.50 Å R-free 0.268 |
| 8YDT Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41 Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–526（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium formate dihydrate
|
Resolution 2.50 Å R-free 0.268 |
| 8YDU Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with CeSPIACE Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M BIS-Tris (pH 5.5), 0.1 M ammonium acetate, 17% PEG 1000
|
Resolution 1.70 Å R-free 0.252 |
| 8YDV Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES (pH 7.5), 10% PEG 6000, 5% MPD
|
Resolution 2.20 Å R-free 0.221 |
| 8YDV Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 7 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M HEPES (pH 7.5), 10% PEG 6000, 5% MPD
|
Resolution 2.20 Å R-free 0.221 |
| 8YDW Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–526（194 aa）
|
Not recorded | GOL GLYCEROL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M CHES (pH 9.5), 20% PEG 8000
|
Resolution 2.00 Å R-free 0.254 |
| 8YDX Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.2 variant) in complex with CeSPIACE Deposited 2024-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
13–1208（1196 aa）
Chain B
13–1208（1196 aa）
Chain C
13–1208（1196 aa）
|
Mutation：F817P, A892P, A898P, A942P, K986P, V987P Mutation：F817P, A892P, A898P, A942P, K986P, V987P Mutation：F817P, A892P, A898P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.90 Å |
| 8YDY Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 1 Deposited 2024-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
13–1208（1196 aa）
Chain B
13–1208（1196 aa）
Chain C
13–1208（1196 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.00 Å |
| 8YDZ Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 2 Deposited 2024-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
13–1208（1196 aa）
Chain B
13–1208（1196 aa）
Chain C
13–1208（1196 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.20 Å |
| 8YE4 The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
448–456（9 aa）
Fragment：448-456 peptide
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；287 K；8% Tacsimate 7.0, 20% PEG3350
|
Resolution 3.20 Å R-free 0.310 |
| 8YE4 The complex of TCR NYN-I and HLA-A24 bound to SARS-CoV-2 Spike448-456 peptide NYNYLYRLF Deposited 2024-02-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain F
448–456（9 aa）
Fragment：448-456 peptide
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；287 K；8% Tacsimate 7.0, 20% PEG3350
|
Resolution 3.20 Å R-free 0.310 |
| 8YF2 Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with raccoon dog ACE2 (local refinement) Deposited 2024-02-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 8YFT Cryo-EM structure of SARS-CoV-2 alpha variant spike protein in complex with raccoon dog ACE2 (local refinement) Deposited 2024-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：RBD domain
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 8YKG Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (1-up state) Deposited 2024-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
12–1210（1199 aa）
Chain B
12–1210（1199 aa）
Chain C
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.28 Å |
| 8YKH Structure of SARS-CoV-2 spike RBD in complex with NT-108 scFv Deposited 2024-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
12–1210（1199 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 3.27 Å |
| 8YRO SARS-CoV-2 Delta Spike in complex with JL-8C Deposited 2024-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain D
14–1208（1195 aa）
Chain P
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 8YRP SARS-CoV-2 Delta Spike in complex with JM-1A Deposited 2024-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.64 Å |
| 8YUB Crystal structure of SARS-CoV-2 ConSp RBD in complex with neutralizing antibody CC25.4 Fab Deposited 2024-03-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–529（197 aa）
Fragment：RBD
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 15% (w/v) PEG 6000
|
Resolution 2.49 Å R-free 0.255 |
| 8YUB Crystal structure of SARS-CoV-2 ConSp RBD in complex with neutralizing antibody CC25.4 Fab Deposited 2024-03-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–529（197 aa）
Fragment：RBD
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris pH 8.5, 15% (w/v) PEG 6000
|
Resolution 2.49 Å R-free 0.255 |
| 8YUC Crystal structure of SARS-CoV-2 ConSp RBD in complex with antibodies PDI222 Fab and COVA1-16 Fab Deposited 2024-03-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
334–529（196 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.0 M NH4-sulfate
|
Resolution 4.51 Å R-free 0.308 |
| 8YWE Local refinement of SARS-CoV-2 Omicron BA.2.86 S complexed with Abs G7-Fc Deposited 2024-03-31 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–541（223 aa）
Fragment：RBD domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.69 Å |
| 8YWW The structure of HKU1-B S protein with bsAb1 Deposited 2024-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–1210（1210 aa）
Chain B
1–1210（1210 aa）
Chain C
1–1210（1210 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8YWX the complex structure of the H4B6 Fab with the RBD of Omicron BA.5 S protein Deposited 2024-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
27–1146（1120 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8YZ5 SARS-CoV-2 Delta Spike in complex with Fab of JE-5C Deposited 2024-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
Chain D
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Tris-HCL, 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.93 Å |
| 8YZ6 SARS-CoV-2 Spike (BA.1) in complex with Fab of JH-8B Deposited 2024-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
14–1210（1197 aa）
Chain B
14–1210（1197 aa）
Chain C
14–1210（1197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20mM Tris-HCL, 150mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.55 Å |
| 8YZB BA.2.86 RBD protein in complex with ACE2. Deposited 2024-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
14–1208（1195 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 8YZC Structure of BA.2.86 spike protein in complex with ACE2. Deposited 2024-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 8YZD Structure of JN.1 RBD protein in complex with ACE2. Deposited 2024-04-06 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
14–1208（1195 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 8YZE The JN.1 spike protein (S) in complex with ACE2. Deposited 2024-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 8YZJ The structure of Banal-52 RBD and hACE2 complex Deposited 2024-04-07 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 8YZR The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLL(EG.5.1) Deposited 2024-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M MES monohydrate pH 6.0, 20% (w/v) Polyethylene glycol 2,000
|
Resolution 1.80 Å R-free 0.262 |
| 8YZW The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRLF(BA.2.86) Deposited 2024-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Sodium citrate tribasic dihydrate , 18% (w/v) Polyethylene glycol 3350
|
Resolution 2.36 Å R-free 0.278 |
| 8YZW The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRLF(BA.2.86) Deposited 2024-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M Sodium citrate tribasic dihydrate , 18% (w/v) Polyethylene glycol 3350
|
Resolution 2.36 Å R-free 0.278 |
| 8YZZ The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYLYRLF(Prototype) Deposited 2024-04-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M Sodium citrate tribasic dihydrate ,18%w/v Polyethylene glycol 3350
|
Resolution 1.88 Å R-free 0.224 |
| 8Z05 The structure of HLA-A*0201 complex with peptide from SARS-CoV-2 N222-230 LLLDRLNKL(BA.2.86/JN.1) Deposited 2024-04-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1181–1189（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium citrate tribasic dihydrate pH 5.5, 18% (w/v) Polyethylene glycol 3,350
|
Resolution 1.96 Å R-free 0.275 |
| 8Z06 The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYDYWYRSF(JN.1) Deposited 2024-04-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES monohydrate pH 6.0, 14% (w/v) Polyethylene glycol 4,000
|
Resolution 2.39 Å R-free 0.232 |
| 8Z07 The structure of HLA-A*2402 complex with peptide from SARS-CoV-2 S448-456 NYNYRYRLF(Delta/BA.5.2) Deposited 2024-04-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
448–456（9 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M MES monohydrate pH 6.0, 14% (w/v) Polyethylene glycol 4,000
|
Resolution 2.70 Å R-free 0.289 |
| 8Z2E Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD Deposited 2024-04-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain E
319–529（211 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Ammonium phosphate dibasic
20% w/v Polyethylene glycol 3,350
|
Resolution 2.30 Å R-free 0.234 |
| 8Z3W Cryo-EM structure of SARS-CoV-2 D614G S with one ACE2 receptor binding (RB1) in prefusion conformation Deposited 2024-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 8Z4X Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion conformation Deposited 2024-04-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 8Z64 Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation (focused refinement of NTD-SD1-RBD-ACE2) Deposited 2024-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.53 Å |
| 8Z6A Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation Deposited 2024-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.99 Å |
| 8Z6Q SARS-CoV-2 XBB.1.16 Spike in complex with CYFN1006-1(S-CYFN1006-1 dimer trimer). Deposited 2024-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
Chain J
14–1208（1195 aa）
Chain K
14–1208（1195 aa）
Chain L
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.41 Å |
| 8Z6R Structure of XBB.1.16 S trimer with 3 down-RBDs complex with antibody CYFN1006-1. Deposited 2024-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.87 Å |
| 8Z6S Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1. Deposited 2024-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.84 Å |
| 8Z6T Structure of XBB.1.16 RBD in complex with antibody CYFN1006-1. Deposited 2024-04-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.92 Å |
| 8Z6U SARS-CoV-2 EG.5.1 Spike in complex with CYFN1006-2(S-CYFN1006-2 dimer trimer). Deposited 2024-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
Chain D
14–1208（1195 aa）
Chain E
14–1208（1195 aa）
Chain F
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.83 Å |
| 8Z6W Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2. Deposited 2024-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 8Z6X Structure of EG.5.1 RBD in complex with antibody CYFN1006-2. Deposited 2024-04-19 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Fragment：RBD,RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.96 Å |
| 8Z7B Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2) Deposited 2024-04-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 8Z7G Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2) Deposited 2024-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.06 Å |
| 8Z7L Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of S-bottom) Deposited 2024-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.42 Å |
| 8Z7P Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) Deposited 2024-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.45 Å |
| 8Z86 BA.5 RBD in complex with CR9 Deposited 2024-04-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–528（201 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.87 Å |
| 8Z9L Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2 Deposited 2024-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
333–527（195 aa）
Fragment：RBD domain
Chain R
333–527（195 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1M HEPES pH7.5, 10% w/v Polyethylene 8000, 8% v/v Ethylene glycol
|
Resolution 3.60 Å R-free 0.277 |
| 8Z9L Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2 Deposited 2024-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain L
333–527（195 aa）
Fragment：RBD domain
Chain X
333–527（195 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.1M HEPES pH7.5, 10% w/v Polyethylene 8000, 8% v/v Ethylene glycol
|
Resolution 3.60 Å R-free 0.277 |
| 8ZBQ Local map of Omicron Subvariant JN.1 RBD with ACE2 Deposited 2024-04-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
336–518（183 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 8ZBY SARS-CoV-2 Omicron BA.1 spike trimer (x2-4P) in complex with 3 D1F6 Fabs (0 RBD up) Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：681-684del, G413C, F817P, A892P, A899P, A942P, V987C Mutation：681-684del, G413C, F817P, A892P, A899P, A942P, V987C Mutation：681-684del, G413C, F817P, A892P, A899P, A942P, V987C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.67 Å |
| 8ZBZ SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up) Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.71 Å |
| 8ZC0 SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up) Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.17 Å |
| 8ZC1 SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region Deposited 2024-04-28 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
332–527（196 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.17 Å |
| 8ZC2 SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
Chain E
14–1211（1198 aa）
Chain F
14–1211（1198 aa）
|
Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.82 Å |
| 8ZC3 SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (1 RBD up) Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.69 Å |
| 8ZC4 SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with 3 D1F6 Fabs (2 RBD up) Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 8ZC5 SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, focused refinement of RBD region Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
332–527（196 aa）
Fragment：RBD
Chain B
332–527（196 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.91 Å |
| 8ZC6 SARS-CoV-2 Omicron BA.4 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate Deposited 2024-04-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
Chain D
14–1211（1198 aa）
Chain E
14–1211（1198 aa）
Chain F
14–1211（1198 aa）
|
Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P Mutation：681-684del, F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.85 Å |
| 8ZER Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350
|
Resolution 3.10 Å R-free 0.283 |
| 8ZER Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350
|
Resolution 3.10 Å R-free 0.283 |
| 8ZER Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350
|
Resolution 3.10 Å R-free 0.283 |
| 8ZER Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350
|
Resolution 3.10 Å R-free 0.283 |
| 8ZER Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 25% PEG 3350
|
Resolution 3.10 Å R-free 0.283 |
| 8ZES Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–541（209 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.15 M DL-Malic acid pH 7.0, 0.1 M Imidazole pH 7.0, 22% PEG MME 550
|
Resolution 3.70 Å R-free 0.269 |
| 8ZES Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–541（209 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.15 M DL-Malic acid pH 7.0, 0.1 M Imidazole pH 7.0, 22% PEG MME 550
|
Resolution 3.70 Å R-free 0.269 |
| 8ZES Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–541（209 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.15 M DL-Malic acid pH 7.0, 0.1 M Imidazole pH 7.0, 22% PEG MME 550
|
Resolution 3.70 Å R-free 0.269 |
| 8ZES Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
333–541（209 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.15 M DL-Malic acid pH 7.0, 0.1 M Imidazole pH 7.0, 22% PEG MME 550
|
Resolution 3.70 Å R-free 0.269 |
| 8ZES Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody Deposited 2024-05-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain I
333–541（209 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；288 K；0.15 M DL-Malic acid pH 7.0, 0.1 M Imidazole pH 7.0, 22% PEG MME 550
|
Resolution 3.70 Å R-free 0.269 |
| 8ZHD SARS-CoV-2 spike trimer (6P) in complex with two R1-26 Fabs Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.41 Å |
| 8ZHE SARS-CoV-2 spike trimer (6P) in complex with three R1-26 Fabs Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 8ZHF SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, head-to-head aggregate Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
Chain D
11–1208（1198 aa）
Chain E
11–1208（1198 aa）
Chain I
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 60 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.26 Å |
| 8ZHG SARS-CoV-2 spike trimer (6P) in complex with R1-26 Fab, focused refinement of RBD-Fab region Deposited 2024-05-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
11–1208（1198 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.51 Å |
| 8ZHH SARS-CoV-2 spike trimer (6P) in complex with two H18 Fabs Deposited 2024-05-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.55 Å |
| 8ZHI SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.05 Å |
| 8ZHJ SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C1 symmetry) Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
Chain G
11–1208（1198 aa）
Chain H
11–1208（1198 aa）
Chain I
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 66 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.45 Å |
| 8ZHK SARS-CoV-2 spike trimer (6P) in complex with three H18 Fabs, head-to-head aggregate (C3 symmetry) Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
Chain G
11–1208（1198 aa）
Chain H
11–1208（1198 aa）
Chain I
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 66 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.30 Å |
| 8ZHL SARS-CoV-2 spike trimer (6P) in complex with two H18 and two R1-32 Fabs Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.96 Å |
| 8ZHM SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.39 Å |
| 8ZHN SARS-CoV-2 spike trimer (6P) in complex with three H18 and three R1-32 Fabs (one RBD rotated) Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 15 PDB declaration: pentadecameric |
Chain A
11–1208（1198 aa）
Chain B
11–1208（1198 aa）
Chain C
11–1208（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.12 Å |
| 8ZHO SARS-CoV-2 S1 in complex with H18 and R1-32 Fab Deposited 2024-05-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
11–676（666 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.54 Å |
| 8ZHP Dimer of SARS-CoV-2 S1 in complex with H18 and R1-32 Fabs Deposited 2024-05-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric |
Chain A
11–676（666 aa）
Chain C
11–676（666 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 8ZPP Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab Deposited 2024-05-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 8ZPQ Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab Deposited 2024-05-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na HEPES, pH7.0, 10% w/v PEG6000
|
Resolution 2.75 Å R-free 0.281 |
| 8ZPQ Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab Deposited 2024-05-31 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Na HEPES, pH7.0, 10% w/v PEG6000
|
Resolution 2.75 Å R-free 0.281 |
| 8ZRD The complex structure of SARS-CoV-2 RBD and llama single-domain antibody S4 Deposited 2024-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–529（211 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1M citrate at pH 5.0 and 20% PEG6000
|
Resolution 2.71 Å R-free 0.295 |
| 8ZRD The complex structure of SARS-CoV-2 RBD and llama single-domain antibody S4 Deposited 2024-06-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–529（211 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1M citrate at pH 5.0 and 20% PEG6000
|
Resolution 2.71 Å R-free 0.295 |
| 8ZV9 Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF Deposited 2024-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
448–456（9 aa）
|
Mutation：Y453F | EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；20% PEG8000, 0.1 M HEPES 7.5
|
Resolution 2.60 Å R-free 0.289 |
| 8ZV9 Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF Deposited 2024-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
448–456（9 aa）
|
Mutation：Y453F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；20% PEG8000, 0.1 M HEPES 7.5
|
Resolution 2.60 Å R-free 0.289 |
| 8ZV9 Complex structure of HLA2402 with recognizing SARS-CoV-2 Y453F epitope NYNYLFRLF Deposited 2024-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain I
448–456（9 aa）
|
Mutation：Y453F | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；20% PEG8000, 0.1 M HEPES 7.5
|
Resolution 2.60 Å R-free 0.289 |
| 8ZYF Crystal structure of ZW2G10 Fab in complex with omicron RBD Deposited 2024-06-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
335–529（195 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.2M Ammonium acetate, 0.1M MES pH 6.5, 15% w/v Polyethylene glycol 3,350
|
Resolution 2.60 Å R-free 0.285 |
| 8ZYF Crystal structure of ZW2G10 Fab in complex with omicron RBD Deposited 2024-06-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
335–529（195 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289 K；0.2M Ammonium acetate, 0.1M MES pH 6.5, 15% w/v Polyethylene glycol 3,350
|
Resolution 2.60 Å R-free 0.285 |
| 9ARU COVA2-15 fragment antigen binding in complex with SARS-CoV-2 6P-mut7 S protein Deposited 2024-02-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9ASD VIR-7229 Fab fragment bound the SARS-CoV-2 BA.2.86 spike trimer (local refinement of the BA 2.86 RBD/VIR-7229 VHVL) Deposited 2024-02-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
1–1208（1208 aa）
Fragment：Prefusion-stabilized BA2.86 spike trimer
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9ATO XBB.1.5 spike/Nanosota-3C complex Deposited 2024-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9ATP local refinement of XBB.1.5 spike/Nanosota-3C complex Deposited 2024-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9ATQ XBB.1.5 spike/Nanosota-8 complex Deposited 2024-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9ATR local refinement of XBB.1.5 spike/Nanosota-8 complex Deposited 2024-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 9AU2 VIR-7229 Fab fragment bound the BA.2.86 spike trimer (global refinement) Deposited 2024-02-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Fragment：Prefusion-stabilized BA2.86 spike trimer
Chain B
1–1208（1208 aa）
Fragment：Prefusion-stabilized BA2.86 spike trimer
Chain C
1–1208（1208 aa）
Fragment：Prefusion-stabilized BA2.86 spike trimer
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 29 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9AYW SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 1 (S-GSAS-Omicron-EG.5.1) Deposited 2024-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9AYX SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 2 (S-GSAS-Omicron-EG.5.1) Deposited 2024-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9AYY SARS-CoV-2 Omicron-EG.5.1 3-RBD down Spike Protein Trimer 3 (S-GSAS-Omicron-EG.5.1) Deposited 2024-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9B0Y SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation Deposited 2024-03-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.32 Å |
| 9B2V SARS CoV-2 Spike protein Ectodomain with internal tag, 1RBD-up conformation Deposited 2024-03-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.55 Å |
| 9B4X SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation (SPIKE-AXA) Deposited 2024-03-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：;D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P, K1269A, H1271A, strep-tag inserted between residues 18 and 19 ; Mutation：;D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P, K1269A, H1271A, strep-tag inserted between residues 18 and 19 ; Mutation：;D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P, K1269A, H1271A, strep-tag inserted between residues 18 and 19 ; | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 9B82 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15 Deposited 2024-03-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.095 M sodium citrate, pH 5.6, 19% (v/v) 2-propanol, 5% (v/v) glycerol, and 19% (w/v) polyethylene glycol 4000
|
Resolution 3.38 Å R-free 0.295 |
| 9B82 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15 Deposited 2024-03-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.095 M sodium citrate, pH 5.6, 19% (v/v) 2-propanol, 5% (v/v) glycerol, and 19% (w/v) polyethylene glycol 4000
|
Resolution 3.38 Å R-free 0.295 |
| 9B82 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15 Deposited 2024-03-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.095 M sodium citrate, pH 5.6, 19% (v/v) 2-propanol, 5% (v/v) glycerol, and 19% (w/v) polyethylene glycol 4000
|
Resolution 3.38 Å R-free 0.295 |
| 9B82 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15 Deposited 2024-03-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.095 M sodium citrate, pH 5.6, 19% (v/v) 2-propanol, 5% (v/v) glycerol, and 19% (w/v) polyethylene glycol 4000
|
Resolution 3.38 Å R-free 0.295 |
| 9B82 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15 Deposited 2024-03-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.095 M sodium citrate, pH 5.6, 19% (v/v) 2-propanol, 5% (v/v) glycerol, and 19% (w/v) polyethylene glycol 4000
|
Resolution 3.38 Å R-free 0.295 |
| 9B82 Crystal structure of SARS-CoV-2 receptor binding domain in complex with neutralizing antibody COVA2-15 Deposited 2024-03-28 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.095 M sodium citrate, pH 5.6, 19% (v/v) 2-propanol, 5% (v/v) glycerol, and 19% (w/v) polyethylene glycol 4000
|
Resolution 3.38 Å R-free 0.295 |
| 9B8F SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 2RBD-up conformation (SPIKE-AXA) Deposited 2024-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：;D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P, K1269A, H1271A, strep-tag inserted between residues 18 and 19 ; Mutation：;D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P, K1269A, H1271A, strep-tag inserted between residues 18 and 19 ; Mutation：;D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P, K1269A, H1271A, strep-tag inserted between residues 18 and 19 ; | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.15 Å |
| 9B9U SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation (SPIKE-KXK) Deposited 2024-04-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G variant, 682-685 RRAR substituted with GSAS, K986P, V987P, H1271K, internal strep-tag near N-terminus Mutation：D614G variant, 682-685 RRAR substituted with GSAS, K986P, V987P, H1271K, internal strep-tag near N-terminus Mutation：D614G variant, 682-685 RRAR substituted with GSAS, K986P, V987P, H1271K, internal strep-tag near N-terminus | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；25 mM Tris(7.5)
150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.86 Å |
| 9BBK SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 2RBD-up conformation (SPIKE-KxK) Deposited 2024-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G variant, 682-685 RRAR substituted with GSAS, K986P, V987P, H1271K Mutation：D614G variant, 682-685 RRAR substituted with GSAS, K986P, V987P, H1271K Mutation：D614G variant, 682-685 RRAR substituted with GSAS, K986P, V987P, H1271K | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；25 mM Tris(7.5)
150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9BD9 SARS CoV-2 full-length WT spike protein, 1RBD-up conformation (SPIKE-WT) Deposited 2024-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P Mutation：D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P Mutation：D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；25 mM Tris(7.5)
150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9BEA Structure of SARS-CoV-2 full-length WT spike protein with internal tag, 2RBD-up conformation (SPIKE-WT) Deposited 2024-04-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Mutation：D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P Mutation：D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P Mutation：D614G variant, residues 682-685 RRAR substituted with GSAS, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；25 mM Tris(7.5)
150 mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.85 Å |
| 9BJ2 Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1533 (local refinement of NTD and C1533) Deposited 2024-04-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9BJ3 Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596 Deposited 2024-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain S
1–1213（1213 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.04 Å |
| 9BJ4 Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C952 Deposited 2024-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9BLL Cryo-EM of RBD(EG5.1)/1301B7 Fab Complex Deposited 2024-04-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain T
27–1210（1184 aa）
Fragment：RBD(EG5.1)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 9BND SARS-CoV-2 spike HexaPro protein in complex with T0A trimeric antagonist Deposited 2024-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–1208（1208 aa）
Chain D
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
|
Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；1x PBS
137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.19 Å |
| 9BNE SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist Deposited 2024-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–1208（1208 aa）
Fragment：extracellular portion
Chain D
1–1208（1208 aa）
Fragment：extracellular portion
Chain F
1–1208（1208 aa）
Fragment：extracellular portion
|
Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；1x PBS
137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.43 Å |
| 9BNF SARS-CoV-2 spike HexaPro protein in complex with T5A trimeric antagonist Deposited 2024-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–1208（1208 aa）
Fragment：extracellular portion
Chain D
1–1208（1208 aa）
Fragment：extracellular portion
Chain F
1–1208（1208 aa）
Fragment：extracellular portion
|
Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；1x PBS:
137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 9BNG SARS-CoV-2 spike HexaPro protein in complex with T18A trimeric antagonist Deposited 2024-05-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
1–1208（1208 aa）
Fragment：extracellular portion
Chain D
1–1208（1208 aa）
Fragment：extracellular portion
Chain F
1–1208（1208 aa）
Fragment：extracellular portion
|
Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) Mutation：hexapro construct (F817P, A892P, A899P, A942P, K986P, V987P, 682-685 mutated from RRAR to GSAS) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；1x PBS
137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.73 Å |
| 9C44 SARS-CoV-2 S + S2L20 Deposited 2024-06-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 9C45 SARS-CoV-2 S + S2L20 (local refinement of NTD and S2L20 Fab variable region) Deposited 2024-06-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9C6Y Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab Deposited 2024-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
319–534（216 aa）
|
Not recorded | SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.4 M ammonium sulfate, 0.1 M sodium acetate pH 5.1, 2 mM DL-panthenol
|
Resolution 2.68 Å R-free 0.242 |
| 9C6Y Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab Deposited 2024-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
319–534（216 aa）
|
Not recorded | SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.4 M ammonium sulfate, 0.1 M sodium acetate pH 5.1, 2 mM DL-panthenol
|
Resolution 2.68 Å R-free 0.242 |
| 9C7S Cryo EM structure of SARS-COV-2 (BQ 1.1) RBD in complex with Fab COV2-3891 (local refine) Deposited 2024-06-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
322–589（268 aa）
Fragment：RBD
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9C7X Crystal structure of SARS-CoV-2 antibody 1H06 in complex with a HR2 peptide Deposited 2024-06-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1179–1197（19 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；88 mM Tris (pH 7.0), 31% PEG monomethyl ether 2000
|
Resolution 1.96 Å R-free 0.215 |
| 9CB0 SARS-CoV-2 S protein - Accum modified Deposited 2024-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1213（1198 aa）
Chain B
16–1213（1198 aa）
Chain C
16–1213（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9CCI Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2 Deposited 2024-06-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.65 Å |
| 9CCJ Dissecting human monoclonal antibody responses from mRNA and protein-based booster vaccinations against XBB1.5 SARS-CoV-2 Deposited 2024-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.37 Å |
| 9CFE Cryo-EM Local Refinement of Antibody 19-77 in complex with prefusion SARS-CoV-2 Spike glycoprotein RBD Deposited 2024-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
335–527（193 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 9CFF Cryo-EM Refinement of Antibody 19-77 in complex with SARS-CoV-2 HK.3 RBD Deposited 2024-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9CFG Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 HK.3 RBD Deposited 2024-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9CFH Cryo-EM Refinement of Antibody 19-77 R71V in complex with SARS-CoV-2 JD.1.1 RBD Deposited 2024-06-27 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
319–537（219 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9CO6 BA.5 spike/Nanosota-9 complex Deposited 2024-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
7–1225（1219 aa）
Chain B
7–1225（1219 aa）
Chain C
7–1225（1219 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.01 Å |
| 9CO7 Local refinement of BA.5 spike/Nanosota-9 complex Deposited 2024-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
14–1216（1203 aa）
Chain B
14–1216（1203 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.32 Å |
| 9CO8 JN.1 spike/Nanosota-9 complex Deposited 2024-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
28–1211（1184 aa）
Chain B
28–1211（1184 aa）
Chain C
28–1211（1184 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.99 Å |
| 9CO9 Local refinement of JN.1 spike/Nanosota-9 complex Deposited 2024-07-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–1216（1216 aa）
Chain B
1–1216（1216 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 9CPP Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-17 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | CIT CITRIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 3.83), 25% (v/v) polyethylene glycol 200, and 9% (w/v) polyethylene glycol 6000
|
Resolution 3.19 Å R-free 0.279 |
| 9CPQ Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-44 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
|
Not recorded | CIT CITRIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 3.83), 25% (v/v) polyethylene glycol 200, and 9% (w/v) polyethylene glycol 6000
|
Resolution 2.88 Å R-free 0.251 |
| 9CPR Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-90 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 4.33), 25% (v/v) polyethylene glycol 200, and 7% (w/v) polyethylene glycol 6000
|
Resolution 3.10 Å R-free 0.247 |
| 9CPS Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-91 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | CIT CITRIC ACID × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 4.33), 25% (v/v) polyethylene glycol 200, and 7% (w/v) polyethylene glycol 6000
|
Resolution 3.03 Å R-free 0.253 |
| 9CPT Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies M22-92 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain, UNP residues 333-530
|
Not recorded | CIT CITRIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 4), 25% (v/v) polyethylene glycol 200, and 5% (w/v) polyethylene glycol 6000
|
Resolution 3.51 Å R-free 0.269 |
| 9CPU Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0304 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain (UNP residues 333-530)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Tris, pH 8, 15% v/v ethylene glycol, 1 M lithium chloride, 10% w/v PEG6000
|
Resolution 2.60 Å R-free 0.239 |
| 9CPV Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0614 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain (UNP residues 333-530)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate / citric acid, pH 4.33, 25% v/v PEG200, 6% w/v PEG6000
|
Resolution 3.00 Å R-free 0.262 |
| 9CPW Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-1036 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain (UNP residues 333-530)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate / citric acid, pH 3.83, 25% v/v PEG200, 7% w/v PEG6000
|
Resolution 3.10 Å R-free 0.234 |
| 9CPX Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C03-0138 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain (UNP residues 333-530)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate / citric acid buffer, pH 3.33, 25% v/v PEG200, 9% w/v PEG6000
|
Resolution 2.70 Å R-free 0.271 |
| 9CPY Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies C11-0860 and CC12.3 Deposited 2024-07-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
333–530（198 aa）
Fragment：Receptor binding domain (UNP residues 333-530)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate / citric acid, pH 3.66, 25% v/v PEG200, 8% w/v PEG6000
|
Resolution 3.10 Å R-free 0.250 |
| 9CRC Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 3 closed RBDs Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9CRD Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: B.1 variant 1 open RBD Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9CRE Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 3 closed RBDs Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9CRF Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Alpha (B.1.1.7) variant 1 open RBD Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9CRG Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Gamma (P.1) variant 3 closed RBDs Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9CRH Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Delta (B.1.617.2) variant 3 closed RBDs Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9CRI Cryo-EM structure of SARS-CoV-2 Spike Proteins on intact virions: Mu (B.1.621) variant 3 closed RBDs Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1273（1273 aa）
Chain B
1–1273（1273 aa）
Chain C
1–1273（1273 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9CSS Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, 1UP RBD conformation Deposited 2024-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.72 Å |
| 9CT2 Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, All RBD down conformation, State-3 Deposited 2024-07-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9CVH Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, 1RBD UP, State-2 Deposited 2024-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.76 Å |
| 9CXE SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation -C1 Deposited 2024-07-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS Mutation：K986P, V987P, 682-685 RRAR mutated to GSAS | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.48 Å |
| 9D8H JN.1 SARS-COV-2 Spike 3-down conformation Deposited 2024-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1273（1246 aa）
Chain B
28–1273（1246 aa）
Chain C
28–1273（1246 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9D8I JN.1 SARS-COV-2 Spike 1-up conformation Deposited 2024-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1273（1246 aa）
Chain B
28–1273（1246 aa）
Chain C
28–1273（1246 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9D8K KP.2 SARS-COV-2 Spike 1-up conformation Deposited 2024-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1273（1246 aa）
Chain B
28–1273（1246 aa）
Chain C
28–1273（1246 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9D8L KP.2 SARS-COV-2 Spike 2-up conformation Deposited 2024-08-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
28–1273（1246 aa）
Chain B
28–1273（1246 aa）
Chain C
28–1273（1246 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9DHY Structure of SARS-CoV-2 spike in complex with antibody Fab COVIC-154 Deposited 2024-09-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain C
14–1208（1195 aa）
Chain F
14–1208（1195 aa）
Chain K
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；TBS buffer pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9DSG Crystal structure of the SARS-CoV-2 RBD in complex with the cow antibody P2 Deposited 2024-09-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–533（206 aa）
Fragment：Receptor-Binding Domain
|
Not recorded | CIT CITRIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1 M Citric acid pH 3.5,
25% w/v Polyethylene glycol 3,350
|
Resolution 2.40 Å R-free 0.263 |
| 9DSL Structure of the SARS-CoV-2 S 6P trimer in complex with the cow antibody 99 Fab Deposited 2024-09-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：Spike 6P construct, arginines in the furin site deleted Mutation：Spike 6P construct, arginines in the furin site deleted Mutation：Spike 6P construct, arginines in the furin site deleted | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 36 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9ECZ Cryo-EM structure of SARS-CoV-2 spike protein in complex with human neutralizing antibody WRAIR-2008 (focused refinement of NTD and WRAIR-2008) Deposited 2024-11-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS + 2% v/v glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.89 Å |
| 9ELE Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 RBD in complex with human ACE2 (local refinement of RBD and hACE2) Deposited 2024-12-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
318–527（210 aa）
Fragment：receptor-binding domain (UNP residues 318-527)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9ELF Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein in complex with human ACE2 Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
1–1208（1208 aa）
Chain F
1–1208（1208 aa）
Chain G
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 26 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.88 Å |
| 9ELG Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike RBD and NTD (local refinement of RBD and NTD) Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–293（293 aa）
Fragment：N-terminal domain (UNP residues 1-293)
Chain C
318–590（273 aa）
Fragment：receptor-binding domain (UNP residues 318-590)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.71 Å |
| 9ELH Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (one RBD up state) Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9ELI Cryo-EM structure of SARS-CoV-2 Omicron KP.3.1.1 spike protein (closed state) Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.82 Å |
| 9ELN Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+S31 deletion spike protein (one RBD up state) Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.93 Å |
| 9ELO Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11+S31 deletion spike protein (closed state) Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.74 Å |
| 9ELP Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11.1+S31 deletion spike protein (one RBD up state) Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.94 Å |
| 9ELQ Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11.1+S31 deletion spike protein (closed state) Deposited 2024-12-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.64 Å |
| 9F9Y SARS-CoV-2 BA-2.87.1 Spike ectodomain Deposited 2024-05-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1183（1183 aa）
Chain B
1–1183（1183 aa）
Chain C
1–1183（1183 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9FC2 The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4. Deposited 2024-05-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
332–534（203 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；22,5 % PEG 8000, 100mM NaAc pH 4.5, 200mM NaCl
|
Resolution 1.21 Å R-free 0.170 |
| 9FCM Single-domain antibody binding the SARS-COV2 S2 Deposited 2024-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain D
1159–1211（53 aa）
Chain E
1159–1211（53 aa）
Chain F
1159–1211（53 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M magnesium chloride hexahydrate, 0.1 M sodium citrate pH 5.0, and 15% PEG4000
|
Resolution 1.94 Å R-free 0.247 |
| 9FGR SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement) Deposited 2024-05-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9FGS SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv41N (focused refinement) Deposited 2024-05-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 9FGT SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76 (focused refinement) Deposited 2024-05-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9FGU SARS-CoV-2 (B.1.1.529/Omicron variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement) Deposited 2024-05-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；PBS
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 9FJK Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 Deposited 2024-05-31 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；TBS, pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.84 Å |
| 9FMW Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6 Deposited 2024-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1207（1207 aa）
Chain B
1–1207（1207 aa）
Chain C
1–1207（1207 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；TBS, pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9FR3 Structure of the SARS-CoV-2 spike glycoprotein in complex with nanobody 7F Deposited 2024-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain D
14–1208（1195 aa）
Chain G
14–1208（1195 aa）
Chain H
14–1208（1195 aa）
Chain J
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9FR4 Structure of the SARS-CoV-2 spike glycoprotein in complex with nanobody 7F (local refinement) Deposited 2024-06-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
14–1208（1195 aa）
Chain D
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9GDX SARS-CoV-2 Spike protein Beta Variant at 4C structural flexibility / heterogeneity analyses Deposited 2024-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9GDY SARS-CoV-2 Spike protein Beta Variant at 37C structural flexibility / heterogeneity analyses Deposited 2024-08-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9GXE Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule Deposited 2024-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1146（1133 aa）
Chain B
14–1146（1133 aa）
Chain C
14–1146（1133 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 STE STEARIC ACID × 3 KZ0 2,4,6-tris(chloromethyl)-1,3,5-triazine × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.30 Å |
| 9GXG Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule Deposited 2024-09-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1146（1133 aa）
Chain B
14–1146（1133 aa）
Chain C
14–1146（1133 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 STE STEARIC ACID × 3 R06 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone × 3 KZ0 2,4,6-tris(chloromethyl)-1,3,5-triazine × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 1.92 Å |
| 9H6U SARS-CoV-2 S protein in complex with pT1679 Fab Deposited 2024-10-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
| 9IB0 Cryo-EM consensus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody Deposited 2025-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9IB1 Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody Deposited 2025-02-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9IB2 Cryo-EM consensus map of prefusion SARS-CoV-2 spike (RBDs: 2 up & 1 down) bound to RBD-targeting MO176-117 antibody Deposited 2025-02-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9IB3 Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 2 up & 1 down) bound to RBD-targeting MO176-117 antibody Deposited 2025-02-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9IQP Crystal structure of the Wuhan SARS-CoV-2 Spike RBD (319-541) complexed with 1p1B10 nanobody Deposited 2024-07-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES monohydrate pH 6.0, 20% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.55 Å R-free 0.208 |
| 9IU1 Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state) Deposited 2024-07-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
28–1210（1183 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P, R682G, R683S, R685G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE；blotting time 5 s and blotting force 5.
|
Resolution 4.30 Å |
| 9IUP KP.3 RBD in complex with ACE2 Deposited 2024-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9IUQ KP.2 RBD in complex with ACE2 Deposited 2024-07-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
334–524（191 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9IUU JN.1 RBD with Q493E in complex with ACE2 Deposited 2024-07-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–527（195 aa）
|
Mutation：Q493E | ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.29 Å |
| 9J66 Cryo-EM structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment CAV-C65 (local refinement) Deposited 2024-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
333–527（195 aa）
Chain D
333–527（195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 9JEB Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1 Deposited 2024-09-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
333–529（197 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3350, pH 6.0
|
Resolution 2.30 Å R-free 0.206 |
| 9JEB Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1 Deposited 2024-09-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
333–529（197 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；289 K；0.2M Magnesium sulfate heptahydrate, 20% w/v Polyethylene glycol 3350, pH 6.0
|
Resolution 2.30 Å R-free 0.206 |
| 9JRC Crystal structure of SARS-CoV-2 receptor-binding domain complexed with squirrel ACE2 Deposited 2024-09-29 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M Ammonium chloride, 20% w/v Polyethylene glycol 3350
|
Resolution 3.16 Å R-free 0.229 |
| 9JS4 Cryo-EM structure of neutralizing antibody 8G3 in complex with BA.1 RBD Deposited 2024-09-30 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
16–1207（1192 aa）
Fragment：RBD domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 5.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9JTE Crystal structure of SARS-CoV-2 receptor binding domain complexed with fox ACE2 Deposited 2024-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M Ammonium sulfate, 20% w/v Polyethylene glycol 3350
|
Resolution 3.66 Å R-free 0.249 |
| 9JTE Crystal structure of SARS-CoV-2 receptor binding domain complexed with fox ACE2 Deposited 2024-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
333–527（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2M Ammonium sulfate, 20% w/v Polyethylene glycol 3350
|
Resolution 3.66 Å R-free 0.249 |
| 9K6J Crystal structure of SARS-CoV-2 WT RBD bound with P5-1C8 Fab Deposited 2024-10-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
319–537（219 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291.15 K；0.2 M Ammonium phosphate dibasic,28% w/v Polyethylene glycol 3,350
|
Resolution 2.39 Å R-free 0.283 |
| 9K6Y Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with H4 Fab (local refinement) Deposited 2024-10-22 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.67 Å |
| 9KT3 Structure of EG.5.1 S trimer with 2 down-RBDs complex with antibody CYFN1006-2. Deposited 2024-12-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.63 Å |
| 9KUD Crystal structure of SARS-CoV-2 JN.1 variant RBD complexed with squirrel ACE2 Deposited 2024-12-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
332–527（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium malonate pH 6.0 20% w/v Polyethylene glycol 3,350
|
Resolution 3.14 Å R-free 0.281 |
| 9KUD Crystal structure of SARS-CoV-2 JN.1 variant RBD complexed with squirrel ACE2 Deposited 2024-12-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
332–527（196 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium malonate pH 6.0 20% w/v Polyethylene glycol 3,350
|
Resolution 3.14 Å R-free 0.281 |
| 9KVD Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 3G5, 4H5 and 4C11 Deposited 2024-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain C
334–527（194 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 9KVE Cryo-EM structure of SARS-CoV-2 prototype spike protein in complex with triple-nAb 4H1, 4A5 and 4C1 Deposited 2024-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain C
334–527（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9KVF Cryo-EM structure of SARS-CoV-2 EG.1 spike protein in complex with triple-nAb 4A5, 4C1 and 2E10 Deposited 2024-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain G
317–600（284 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9KVJ Cryo-EM structure of SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 (local refinement) Deposited 2024-12-05 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.82 Å |
| 9KVK Cryo-EM structure of SARS-CoV-2 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Deposited 2024-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain G
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.44 Å |
| 9KVQ Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with three-nAb 8H12, 3E2 and 1C4 Deposited 2024-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain G
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.95 Å |
| 9KVT Cryo-EM structure of SARS-CoV-2 BA.2 spike protein in complex with triple-nAb 8H12, 3E2 and 1C4 (local refinement) Deposited 2024-12-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain G
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9KWY Cryo-EM structure of SARS-CoV-2 RBD in complex with ACE2 and mAb 1C4 Deposited 2024-12-06 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain G
334–517（184 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.82 Å |
| 9KZD The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-171 Deposited 2024-12-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.65 Å |
| 9KZE The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-183 Deposited 2024-12-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9KZZ Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-171 Deposited 2024-12-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.18 Å |
| 9L05 The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198 Deposited 2024-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.24 Å |
| 9L07 The local refined map of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203 Deposited 2024-12-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.28 Å |
| 9L15 Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-203 Deposited 2024-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9L2L Structure of SARS-CoV-2 EG.5.1 Variant Spike protein complexed with antibody XGi-198 Deposited 2024-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
Chain D
14–1208（1195 aa）
Chain E
14–1208（1195 aa）
Chain F
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.98 Å |
| 9L3I Cryo-EM structure of SARS-CoV-2 BA.2.75 Spike Protein complex with a potent broad-spectrum macrocyclic peptide inhibitor 6L3-3P11K Deposited 2024-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
28–1144（1117 aa）
Chain B
28–1144（1117 aa）
Chain C
28–1144（1117 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9L3Q Cryo-EM structure of SARS-CoV-2 PT Spike Protein complex with a potent broad-spectrum macrocyclic peptide inhibitor 6L3-3P11K Deposited 2024-12-19 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
14–1208（1195 aa）
Chain B
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.70 Å |
| 9L6C Cryo-EM structure of Delta RBD complexed with ConD-852, P2C-1F11 and S304 Fabs Deposited 2024-12-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain E
333–526（194 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS, pH=7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.33 Å |
| 9LAE Locally refined region of SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2. Deposited 2025-01-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain G
319–541（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.46 Å |
| 9LBS Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs Deposited 2025-01-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain F
337–517（181 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；blot time:4s
wait time:2.5s
blot force:0
|
Resolution 3.41 Å |
| 9LD2 Cryo-EM structure of SARS-CoV-2 wide-type S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab (focused refinement of the S2-76E1) Deposited 2025-01-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.73 Å |
| 9LDJ Cryo-EM structure of SARS-CoV-2 wide-type S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab Deposited 2025-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 48 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.21 Å |
| 9LDS Crystal structure of nanobody H145 bound to SARS-CoV-2 spike stem-helix Deposited 2025-01-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1139–1153（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 70% v/v (+/-)-2-Methyl-2,4-pentanediol
|
Resolution 1.60 Å R-free 0.202 |
| 9LDS Crystal structure of nanobody H145 bound to SARS-CoV-2 spike stem-helix Deposited 2025-01-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1139–1153（15 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M HEPES pH 7.5, 70% v/v (+/-)-2-Methyl-2,4-pentanediol
|
Resolution 1.60 Å R-free 0.202 |
| 9LH2 Crystal structure of SARS-CoV-2 spike receptor-binding domain (Delta) in complex with pH-dependent nanobody MNb-11. Deposited 2025-01-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
320–537（218 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；0.09M NPS, 0.1M Tris (base), 0.1M BICINE, pH 8.5, 20% v/v PEG 500* MME, 10 % w/v PEG 20000
|
Resolution 2.30 Å R-free 0.236 |
| 9LH2 Crystal structure of SARS-CoV-2 spike receptor-binding domain (Delta) in complex with pH-dependent nanobody MNb-11. Deposited 2025-01-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
320–537（218 aa）
Fragment：Receptor-binding domain (RBD)
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；0.09M NPS, 0.1M Tris (base), 0.1M BICINE, pH 8.5, 20% v/v PEG 500* MME, 10 % w/v PEG 20000
|
Resolution 2.30 Å R-free 0.236 |
| 9LOY Cryo-EM structure of SARS-CoV-2 JN.1 spike glycoprotein in complex with F61R2-780 Fab Deposited 2025-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P Mutation：F817P,A892P,A899P,A942P,K986P,V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 9LOZ Cryo-EM structure of SARS-CoV-2 JN.1 RBD in complex with F61R2-780 Fab Deposited 2025-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
333–527（195 aa）
Fragment：RBD domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.55 Å |
| 9LP0 Cryo-EM structure of SARS-CoV-2 KP.3.1.1 spike glycoprotein in complex with F61R2-780 Fab Deposited 2025-01-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.61 Å |
| 9LP1 Cryo-EM structure of SARS-CoV-2 KP.3.1.1 RBD in complex with F61R2-780 Fab Deposited 2025-01-23 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
334–528（195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.47 Å |
| 9LS3 S-ECD of SARS-CoV-2 Delta variant in complex with Fab854 Deposited 2025-02-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9LVI Cryo-EM structure of SARS-CoV-2 spike protein Deposited 2025-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.86 Å |
| 9LVS Cryo-EM structure of the SARS-CoV-2 spike protein in complex with S416 Deposited 2025-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EZO 2-[(E)-[[4-(2-chlorophenyl)-1,3-thiazol-2-yl]-methyl-hydrazinylidene]methyl]benzoic acid × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 2.95 Å |
| 9LYO Alpha SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue. Deposited 2025-02-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
16–1208（1193 aa）
Chain B
16–1208（1193 aa）
Chain C
16–1208（1193 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.07 Å |
| 9MI3 Cryo-EM structure of SARS-CoV-2 spike protein in complex with neutralizing human antibody WRAIR-2008 Deposited 2024-12-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1208（1195 aa）
Chain C
14–1208（1195 aa）
Chain K
14–1208（1195 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；PBS + 2% v/v glycerol
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.23 Å |
| 9ML4 Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-A10 Fab Deposited 2024-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9ML5 Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-B8 Fab Deposited 2024-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9ML6 Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C9 Fab Deposited 2024-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 45 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9ML7 Structure of the SARS-CoV-2 Spike 6P in complex with the rabbit M8b-C10 Fab Deposited 2024-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1213（1213 aa）
Chain B
1–1213（1213 aa）
Chain C
1–1213（1213 aa）
|
Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P Mutation：F817P, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9ML8 Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab Deposited 2024-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–533（206 aa）
Fragment：Receptor-Binding Domain
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M lithium sulfate
0.1 sodium citrate
20% (w/v) PEG 1,000
|
Resolution 2.40 Å R-free 0.247 |
| 9ML8 Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab Deposited 2024-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
328–533（206 aa）
Fragment：Receptor-Binding Domain
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M lithium sulfate
0.1 sodium citrate
20% (w/v) PEG 1,000
|
Resolution 2.40 Å R-free 0.247 |
| 9ML8 Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab Deposited 2024-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
328–533（206 aa）
Fragment：Receptor-Binding Domain
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M lithium sulfate
0.1 sodium citrate
20% (w/v) PEG 1,000
|
Resolution 2.40 Å R-free 0.247 |
| 9ML8 Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-B1 Fab Deposited 2024-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
328–533（206 aa）
Fragment：Receptor-Binding Domain
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M lithium sulfate
0.1 sodium citrate
20% (w/v) PEG 1,000
|
Resolution 2.40 Å R-free 0.247 |
| 9ML9 Crystal structure of the SARS-CoV-2 RBD in complex with the rabbit M8b-C9 Fab Deposited 2024-12-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–533（206 aa）
Fragment：Receptor-Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；297 K；2% v/v 1,4-dioxane
0.1M Tris pH 8.0
15% (w/v) PEG 3,350
|
Resolution 2.59 Å R-free 0.257 |
| 9MPW SARS-CoV2 Spike S2 Subunit in complex with M15 Antibody Fragment Deposited 2024-12-31 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain S
686–1208（523 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.37 Å |
| 9MR1 SARS-CoV-2 S2 monomer in complex with R125-61 Fab Deposited 2025-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
698–1161（464 aa）
|
Mutation：F817P, G880C, F888C, A892P, A899P, A942P, T912P, K986P, V987P, T1117C, D1139C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.59 Å |
| 9MR2 SARS-CoV-2 S2 monomer in complex with NICA01A-1401 Fab Deposited 2025-01-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
698–1161（464 aa）
|
Mutation：F817P, G880C, F888C, A892P, A899P, A942P, T912P, K986P, V987P, T1117C, D1139C | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.79 Å |
| 9N2L Cryo-EM structure of locally refined up conformation of SARS-CoV-2 spike protein Receptor Binding Domain Deposited 2025-01-29 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.99 Å |
| 9NVG Structure of SARS-CoV-2 BA.1 spike RBD bound to COV2-3835 Fab Deposited 2025-03-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
|
Mutation：HexaPro construct | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9NXY Cryo-EM structure of SARS-CoV-2 spike S2' trimer Deposited 2025-03-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
686–1273（588 aa）
Chain B
686–1273（588 aa）
Chain C
686–1273（588 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.08 Å |
| 9O5T Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric Rhinolophus sinicus ACE2 Deposited 2025-04-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–536（218 aa）
Fragment：receptor-binding domain (UNP residues 319-536)
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Tris, pH 7.5-8.5, 16-24% PEG6000, 100 mM sodium chloride
|
Resolution 2.90 Å R-free 0.251 |
| 9O5T Crystal structure of chimeric SARS-CoV-2 RBD complexed with chimeric Rhinolophus sinicus ACE2 Deposited 2025-04-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
319–536（218 aa）
Fragment：receptor-binding domain (UNP residues 319-536)
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Tris, pH 7.5-8.5, 16-24% PEG6000, 100 mM sodium chloride
|
Resolution 2.90 Å R-free 0.251 |
| 9O5V Crystal structure of chimeric BANAL-52 RBD complexed with chimeric Rhinolophus sinicus ACE2 Deposited 2025-04-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–536（218 aa）
Fragment：receptor-binding domain (UNP residues 319-536)
|
Not recorded | ZN ZINC ION × 1 NA SODIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Tris, pH 7.5-8.5, 16-24% PEG6000, 100 mM sodium chloride
|
Resolution 3.35 Å R-free 0.266 |
| 9O5V Crystal structure of chimeric BANAL-52 RBD complexed with chimeric Rhinolophus sinicus ACE2 Deposited 2025-04-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
319–536（218 aa）
Fragment：receptor-binding domain (UNP residues 319-536)
|
Not recorded | ZN ZINC ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Tris, pH 7.5-8.5, 16-24% PEG6000, 100 mM sodium chloride
|
Resolution 3.35 Å R-free 0.266 |
| 9OG4 SARS-COV-2-6P-MUT7 S PROTEIN-DY-III-281 complex closed conformation Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 5 s
|
Resolution 3.56 Å |
| 9OG5 SARS-COV-2-6P-MUT7 S PROTEIN-DY-III-281 complex 1 RBD up conformation Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；blotted for 5 s
|
Resolution 3.30 Å |
| 9OG6 Apo SARS-COV-2-6P-MUT7 S PROTEIN closed conformation Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE；blot time of 5 s
|
Resolution 3.14 Å |
| 9OG7 APO SARS-COV-2-6P-MUT7 S PROTEIN 1 RBD UP CONFORMATION Deposited 2025-04-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P Mutation：R682G, R683S, R685S, V705C, F817P, T883C, A892P, A899P, A942P, K986P, V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2；PBS
cryo-EM vitrification conditions
Cryogen ETHANE；5 s blot time.
|
Resolution 3.09 Å |
| 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–533（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 5 PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 4.0), 25% (v/v) polyethylene glycol 200, and 5% (w/v) polyethylene glycol 6000
|
Resolution 2.54 Å R-free 0.254 |
| 9PSN Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-105 and CC12.3 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain T
333–533（201 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 3 PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 4.0), 25% (v/v) polyethylene glycol 200, and 5% (w/v) polyethylene glycol 6000
|
Resolution 2.54 Å R-free 0.254 |
| 9PSO Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-622 and CC12.3 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain E
333–533（201 aa）
|
Not recorded | SO4 SULFATE ION × 11 EDO 1,2-ETHANEDIOL × 7 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 5.0), 1.6 M ammonium sulfate, and 20% (v/v) glycerol
|
Resolution 2.62 Å R-free 0.258 |
| 9PSP Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain T
333–533（201 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 4 EDO 1,2-ETHANEDIOL × 1 1PE PENTAETHYLENE GLYCOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 4.0), 25% (v/v) polyethylene glycol 200, and 5% (w/v) polyethylene glycol 6000
|
Resolution 2.81 Å R-free 0.247 |
| 9PSP Crystal structure of SARS-CoV-2 receptor binding domain in complex with antibodies BoWLB-1173 and CC12.3 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain U
333–533（201 aa）
|
Not recorded | PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M sodium citrate citric acid buffer (pH 4.0), 25% (v/v) polyethylene glycol 200, and 5% (w/v) polyethylene glycol 6000
|
Resolution 2.81 Å R-free 0.247 |
| 9PW4 Structure of V30V4 in complex with SARS-CoV-2 spike Deposited 2025-08-04 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–684（684 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.85 Å |
| 9RN6 Crystal structure of a protein mimic of SARS-CoV-2 spike's HR1 domain in complex with two nanobodies bound to different epitopes Deposited 2025-06-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
915–988（74 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；288 K；0.15 M NaCl, PEG 6000 50% (v/v), 0.1 M Tris/HCl
|
Resolution 2.40 Å R-free 0.263 |
| 9SAT Monoclonal Antibodies from COVID-19 Convalescent Patients Target Cryptic Epitopes for Universal SARS-CoV-2 Neutralization Deposited 2025-08-07 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
319–541（223 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；289.15 K；0.2M Zinc Acetate Dehydrate, 0.1M Sodium Cacodylate Trihydrate, 15% PEG 8000
|
Resolution 2.56 Å R-free 0.275 |
| 9SBB Monoclonal Antibodies from COVID-19 Convalescent Patients Target Cryptic Epitopes for Universal SARS-CoV-2 Neutralization Deposited 2025-08-08 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain R
327–535（209 aa）
|
Not recorded | GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 1 LI LITHIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289.15 K；0.2M Lithium Citrate Tribasic Tetrahydrate, 20% PEG 3350
|
Resolution 2.12 Å R-free 0.230 |
| 9T74 2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: RBD-aptamer) Deposited 2025-11-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric |
Chain B
14–1147（1134 aa）
|
Not recorded | MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.46 Å |
| 9UE6 Cryo-EM structure of SARS-CoV-2 KP.2 spike RBD in complex with ACE2 Deposited 2025-04-08 | Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
333–528（196 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9UG3 Structure of SARS-CoV-2 spike-CD147 complex at 3.75 Angstroms resolution Deposited 2025-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
27–1146（1120 aa）
Chain B
27–1146（1120 aa）
Chain C
27–1146（1120 aa）
|
Mutation：residues 1-1208 Mutation：residues 1-1208 Mutation：residues 1-1208 | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Pbs
|
Resolution 3.75 Å |
| 9UPR Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N103 and S2L20 Fab Deposited 2025-04-28 | Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain F
1–305（305 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.77 Å |
| 9UTF Crystal Structure of SARS-CoV-2 S receptor-binding domain (RBD) in complex XG83 Fab Deposited 2025-05-03 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
321–591（271 aa）
Fragment：receptor binding domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 3.5；288 K；18% PEG 6000, G11. 0.15M Lithium sulfate monohydrate, 0.1M Citric Acid pH 3.5.
|
Resolution 2.95 Å R-free 0.295 |
| 9UXD SARS-CoV2 Spike protein with Fab fragment antibody KXD355,state1 Deposited 2025-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P/A892P/A899P/A942P/K986P/V987P Mutation：F817P/A892P/A899P/A942P/K986P/V987P Mutation：F817P/A892P/A899P/A942P/K986P/V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.03 Å |
| 9UXE SARS-CoV2 Spike protein with Fab fragment antibody KXD355,state2 Deposited 2025-05-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Mutation：F817P/A892P/A899P/A942P/K986P/V987P Mutation：F817P/A892P/A899P/A942P/K986P/V987P Mutation：F817P/A892P/A899P/A942P/K986P/V987P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.17 Å |
| 9UXS The local refine of 3D reconstruction of the complex formed by SARS-CoV2 BA.1 spike glycoprotein and a single-domain antibody Deposited 2025-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
14–1208（1195 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9UYD SARS-CoV-2 Ancestral strain spike S-cred Deposited 2025-05-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
27–1146（1120 aa）
Chain B
27–1146（1120 aa）
Chain F
27–1146（1120 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 2.70 Å |
| 9VLS Cryo-EM structure of SARS-CoV-2 XBB.1.5 S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab (focused refinement of the S2-76E1) Deposited 2025-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.14 Å |
| 9VLT Cryo-EM structure of SARS-CoV-2 XBB.1.5 S trimer in the early fusion intermediate conformation (E-FIC) complexed with ACE2 and 76E1-Fab Deposited 2025-06-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.65 Å |
| 9W14 Cryo-EM structure of SARS-CoV-2 WT spike protein in complex with nAb 1C4 Deposited 2025-07-25 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain G
319–541（223 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.33 Å |
| 9WLA Local refinement region of SARS-CoV-2 spike RBD in complex with antibodies CT1-5. Deposited 2025-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.60 Å |
| 9WLB Local refinement region of SARS-CoV-2 spike RBD in complex with antibodies S309 and CT1-1. Deposited 2025-09-02 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain R
319–541（223 aa）
Fragment：RBD
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.74 Å |
| 9WSP Cryo-EM structure of SARS CoV2 S protein with stabilising mutations Deposited 2025-09-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
27–1147（1121 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.55 Å |
| 9XGO Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain Deposited 2025-10-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain N
15–303（289 aa）
Chain R
323–545（223 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.77 Å |
| 9Y5Y Structure of the Omicron Spike RBD bound by the monobody s19382 (local refinement from dimerized Spike protein ECDs) Deposited 2025-09-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain A
334–528（195 aa）
Fragment：receptor-binding domain
Chain C
334–528（195 aa）
Fragment：receptor-binding domain
Chain E
334–528（195 aa）
Fragment：receptor-binding domain
Chain G
334–528（195 aa）
Fragment：receptor-binding domain
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.16 Å |
| 9YNX Local refinement of Fab-14/SARS-CoV-2 D614G spike complex, Mode IV, Subgroup I conformation Deposited 2025-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
323–527（205 aa）
Chain B
323–527（205 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 9YOK Fab-14/SARS-CoV-2 D614G spike complex, Mode I conformation Deposited 2025-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.56 Å |
| 9YPB Fab-14/SARS-CoV-2 D614G spike complex, Mode IV, subgroup II conformation Deposited 2025-10-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9YPR Fab-14/SARS-CoV-2 D614G spike complex, Mode IV, subgroup I conformation Deposited 2025-10-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric |
Chain A
1–1208（1208 aa）
Chain B
1–1208（1208 aa）
Chain C
1–1208（1208 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.46 Å |
| 9YYU SARS-CoV-2 spike trimer in the early fusion intermediate conformation bound to the VN01H1 Fab (Fab local refinement) Deposited 2025-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：D614G variant, R682S, R683G Mutation：D614G variant, R682S, R683G Mutation：D614G variant, R682S, R683G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9YYV SARS-CoV-2 spike trimer in the early fusion intermediate conformation bound to the VN01H1 Fab (S2 local refinement) Deposited 2025-10-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
14–1211（1198 aa）
Chain B
14–1211（1198 aa）
Chain C
14–1211（1198 aa）
|
Mutation：R682S, R683G Mutation：R682S, R683G Mutation：R682S, R683G | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9Z3K SARS-CoV-2 S2 trimer stabilized in the early fusion intermediate conformation by circular permutation and clamping by gp41 (E-FICs-v1) Deposited 2025-11-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
914–1131（218 aa）
Chain A
703–828（126 aa）
Chain B
914–1131（218 aa）
Chain B
703–828（126 aa）
Chain C
914–1131（218 aa）
Chain C
703–828（126 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9Z80 SARS-CoV-2 S2 in complex with polyclonal Fab_Donor1 Deposited 2025-11-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Homooligomer；Protein × 3 PDB declaration: pentameric |
Chain C
698–1161（464 aa）
Chain D
698–1161（464 aa）
Chain E
698–1161（464 aa）
|
Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.17 Å |
| 9ZDU Crystal structure of SARS-CoV-2 RBD in complex with human Ab401 Fab Deposited 2025-11-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
328–533（206 aa）
Fragment：Receptor-Binding Domain
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.2 M Ammonium phosphate monobasic
20% PEG 3350
|
Resolution 2.60 Å R-free 0.253 |
| 9ZT5 SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor3 Deposited 2025-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
698–1161（464 aa）
Chain D
698–1161（464 aa）
Chain E
698–1161（464 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.21 Å |
| 9ZT6 SARS-CoV-2 S2 in complex with polyclonal Fab-B_Donor8 Deposited 2025-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
698–1161（464 aa）
Chain D
698–1161（464 aa）
Chain E
698–1161（464 aa）
|
Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.83 Å |
| 9ZT7 SARS-CoV-2 S2 in complex with COV2-2509 Deposited 2025-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric |
Chain C
698–1161（464 aa）
Chain D
698–1161（464 aa）
Chain E
698–1161（464 aa）
|
Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W Mutation：S704C, K790C, G880C, F888C, A892P, A899P, A942P, K986P, V987P, T961F, V991W, T998W | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 9ZT8 Stabilized SARS-CoV-2 S2 apo Deposited 2025-12-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
698–1161（464 aa）
Chain B
698–1161（464 aa）
Chain C
698–1161（464 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.75 Å |
2152 other PDB entries and 2471 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SPIKE_SARS2 |
| Isoform | — |
| PDB entities | 3 |
| Chains and sequence ranges | Author chain R； PDBConstruct 7–202； UniProt 333–528 Author chain X； PDBConstruct 7–202； UniProt 333–528 Author chain Y； PDBConstruct 7–202； UniProt 333–528 |
