Spike glycoprotein,Fibritin
Enterobacteria phage T4
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Insufficient information Homooligomer Protein × 3 其他Polymer 15 PDB declaration: trimeric（3） Consistent with protein copy count | Chain A； UniProt 458–484 Chain B； UniProt 458–484 Chain C； UniProt 458–484 | Not recorded | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33 EIC LINOLEIC ACID × 3 | ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE | Resolution 3.10 Å |
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 9JMF | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1AA0 FIBRITIN DELETION MUTANT E (BACTERIOPHAGE T4) Deposited 1997-01-18 | 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
371–483（113 aa）
Fragment：DELETION MUTANT E, DEL(368-486)
|
Not recorded | CL CHLORIDE ION × 3 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；PROTEIN WAS CRYSTALLIZED AT 22OC USING 34% PEG400, 0.1M ZN ACETATE IN 0.1M MES BUFFER AT PH6.0 AS WELL SOLUTION BY MIXING EQUAL AMOUNT OF WELL SOLUTION AND PROTEIN SOLUTION AT 29MG/ML IN A HANGING DROP, vapor diffusion - hanging drop
|
Resolution 2.20 Å R-free 0.259 |
| 1AVY FIBRITIN DELETION MUTANT M (BACTERIOPHAGE T4) Deposited 1997-09-22 | 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
413–486（74 aa）
Fragment：DELETION MUTANT M, RESIDUES 413 - 486 OF THE WILD TYPE
|
Mutation：R416S, S421K, N425I, N428D, T433R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROPS WITH 20MG/ML PROTEIN AND 1.75M LI2SO4, 0.1M TRIS-HCL, PH7.5, AS PRECIPITANT, vapor diffusion - hanging drop
|
Resolution 1.85 Å R-free 0.253 |
| 1AVY FIBRITIN DELETION MUTANT M (BACTERIOPHAGE T4) Deposited 1997-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain B
413–486（74 aa）
Fragment：DELETION MUTANT M, RESIDUES 413 - 486 OF THE WILD TYPE
|
Mutation：R416S, S421K, N425I, N428D, T433R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROPS WITH 20MG/ML PROTEIN AND 1.75M LI2SO4, 0.1M TRIS-HCL, PH7.5, AS PRECIPITANT, vapor diffusion - hanging drop
|
Resolution 1.85 Å R-free 0.253 |
| 1AVY FIBRITIN DELETION MUTANT M (BACTERIOPHAGE T4) Deposited 1997-09-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain C
413–486（74 aa）
Fragment：DELETION MUTANT M, RESIDUES 413 - 486 OF THE WILD TYPE
|
Mutation：R416S, S421K, N425I, N428D, T433R | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROPS WITH 20MG/ML PROTEIN AND 1.75M LI2SO4, 0.1M TRIS-HCL, PH7.5, AS PRECIPITANT, vapor diffusion - hanging drop
|
Resolution 1.85 Å R-free 0.253 |
| 1OX3 crystal structure of mini-fibritin Deposited 2003-04-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
2–81（80 aa）
Fragment：UNP residues 2-81 and 456-484
Chain A
456–484（29 aa）
Fragment：UNP residues 2-81 and 456-484
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；PEG 6000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 303K
|
Resolution 2.00 Å R-free 0.221 |
| 1RFO Trimeric Foldon of the T4 phagehead fibritin Deposited 2003-11-10 | Different construct 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
458–484（27 aa）
Fragment：trimerization domain (residues 457-483)
Chain B
458–484（27 aa）
Fragment：trimerization domain (residues 457-483)
Chain C
458–484（27 aa）
Fragment：trimerization domain (residues 457-483)
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.1；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure 1013
NMR sample composition
0.3 mM Foldon 15N,13C; 5mM phosphate buffer pH 7.1 | 95% H2O/5% D2O
|
Resolution not provided |
| 1V1H Adenovirus fibre shaft sequence N-terminally fused to the bacteriophage T4 fibritin foldon trimerisation motif with a short linker Deposited 2004-04-16 | Different construct 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
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Chain B
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Chain C
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.2 M IMIDAZOLE-MALATE PH 6.0 8% (W/V) PEG 4000
|
Resolution 1.90 Å R-free 0.240 |
| 1V1H Adenovirus fibre shaft sequence N-terminally fused to the bacteriophage T4 fibritin foldon trimerisation motif with a short linker Deposited 2004-04-16 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain D
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Chain E
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Chain F
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.2 M IMIDAZOLE-MALATE PH 6.0 8% (W/V) PEG 4000
|
Resolution 1.90 Å R-free 0.240 |
| 1V1I Adenovirus fibre shaft sequence N-terminally fused to the bacteriophage T4 fibritin foldon trimerisation motif with a long linker Deposited 2004-04-16 | Different construct 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
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Chain B
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
Chain C
457–483（27 aa）
Fragment：SHAFT DOMAIN PLUS FOLDON DOMAIN, RESIDUES 319-392 AND 457-483
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；10 MM HEPES-NAOH PH 7.0 0.2 M MAGNESIUM ACETATE, 20 % (W/V) PEG 3350
|
Resolution 1.90 Å R-free 0.283 |
| 2BSG The modeled structure of fibritin (gpwac) of bacteriophage T4 based on cryo-EM reconstruction of the extended tail of bacteriophage T4 Deposited 2005-05-20 | Different construct 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
1–487（487 aa）
Chain B
1–487（487 aa）
Chain C
1–487（487 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；H2O
cryo-EM vitrification conditions
Cryogen ETHANE；LIQUID ETHANE
|
Resolution 15.00 Å |
| 2IBL Crystal structure of a helper molecule (HT-mf-thromb) based on mini-fibritin (mf) crystal structure (pdb:1OX3). Deposited 2006-09-11 | 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 Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
2–81（80 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 10.5；293 K；30% PEG 400, 0.1 M TrisHCl, 0.2 M magnesium chloride, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
|
Resolution 1.32 Å R-free 0.170 |
| 2KBL NMR Structure of a Monomeric Folding Intermediate Reveals the Structural Basis for Rapid Assembly of an Evolutionary Optimized Trimerization Module Deposited 2008-12-02 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
458–484（27 aa）
Fragment：C-terminal Domain, UNP residues 458-484
|
Mutation：E5R, F22L | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；296.7 K；Ionic strength (raw mmCIF value) 10；Pressure ambient
NMR sample composition
200uM foldon E5R, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition
210uM [U-99% 15N] foldon E5R, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 3A1M A fusion protein of a beta helix region of gene product 5 and the foldon region of bacteriophage T4 Deposited 2009-04-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
Chain D
458–484（27 aa）
Chain E
458–484（27 aa）
Chain F
458–484（27 aa）
|
Mutation：V16L Mutation：V16L Mutation：V16L Mutation：V16L Mutation：V16L Mutation：V16L | K POTASSIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；Ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.268 |
| 3J2O Model of the bacteriophage T4 fibritin based on the cryo-EM reconstruction of the contracted T4 tail containing the phage collar and whiskers Deposited 2012-11-12 | 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
2–487（486 aa）
Chain B
2–487（486 aa）
Chain C
2–487（486 aa）
Chain D
2–487（486 aa）
Chain E
2–487（486 aa）
Chain F
2–487（486 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
50 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 8 mM MgCl2；pH 8；50 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 8 mM MgCl2
cryo-EM vitrification conditions
Cryogen ETHANE；plunged into liquid ethane (homemade plunger)
|
Resolution 25.00 Å |
| 4MMQ Crystal Structure of Prefusion-stabilized RSV F Variant DS Deposited 2013-09-09 | 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 × 6 PDB declaration: hexameric |
Chain B
458–484（27 aa）
|
Mutation：S155C, S290C, I379V, M447V | SO4 SULFATE ION × 18 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.5；298 K；1.4 M K/Na tartrate, 0.1M CHES pH 9.5, 0.2 M LiSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 3.25 Å R-free 0.274 |
| 4MMR Crystal Structure of Prefusion-stabilized RSV F Variant Cav1 at pH 9.5 Deposited 2013-09-09 | 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 × 6 PDB declaration: hexameric |
Chain B
458–484（27 aa）
|
Mutation：S190F, V207L, I379V, M447V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；1.4M sodium potassium tartarate, 0.1M CHES, pH 9.5, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 3.10 Å R-free 0.264 |
| 4MMS Crystal Structure of Prefusion-stabilized RSV F Variant Cav1 at pH 5.5 Deposited 2013-09-09 | 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
458–484（27 aa）
Chain D
458–484（27 aa）
Chain F
458–484（27 aa）
|
Mutation：S190F, V207L, I379V, M447V Mutation：S190F, V207L, I379V, M447V Mutation：S190F, V207L, I379V, M447V | SO4 SULFATE ION × 14 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；1.7 M ammonium sulfate, 0.1 M citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.40 Å R-free 0.214 |
| 4MMT Crystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 at pH 9.5 Deposited 2013-09-09 | 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 × 6 PDB declaration: hexameric |
Chain B
458–484（27 aa）
|
Mutation：S155C, S190F, V207L, S290C, I379V, M447V | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.5；1.8 M Na/K tartrate,
0.2 M LiSO4,
0.1 M CHES pH9.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.05 Å R-free 0.243 |
| 4MMU Crystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1 at pH 5.5 Deposited 2013-09-09 | 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 × 6 PDB declaration: hexameric |
Chain B
458–484（27 aa）
|
Mutation：S155C, S190F, V207L, S290C, I379V, M447V | SO4 SULFATE ION × 12 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PO4 PHOSPHATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；1.8 M Ammonium sulphate
0.1 M citrate pH5.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 3.00 Å R-free 0.228 |
| 4MMV Crystal Structure of Prefusion-stabilized RSV F Variant DS-Cav1-TriC at pH 9.5 Deposited 2013-09-09 | 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 × 6 PDB declaration: hexameric |
Chain B
458–484（27 aa）
|
Mutation：S155C, S190F, V207L, S290C, I379V, M447, VD486H, E487Q, F488W, D489H | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 9.5；293 K；1.4M sodium potassium tartarate, 0.1M CHES, pH 9.5, 0.2M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.81 Å R-free 0.279 |
| 5I08 Prefusion structure of a human coronavirus spike protein Deposited 2016-02-03 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Mutation：R751G, R752G, K753S, R754G, R755S,R751G, R752G, K753S, R754G, R755S Mutation：R751G, R752G, K753S, R754G, R755S,R751G, R752G, K753S, R754G, R755S Mutation：R751G, R752G, K753S, R754G, R755S,R751G, R752G, K753S, R754G, R755S | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE；3 uL sample was applied to grid, blotted, and plunged into liquid ethane.
|
Resolution 4.04 Å |
| 5TDL Crystal structure of prefusion-stabilized bovine RSV fusion glycoprotein (single-chain DS2-v1 variant: strain 391-2 sc9 DS-Cav1 Q98C Q361C) Deposited 2016-09-19 | 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 Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
457–484（28 aa）
|
Mutation：Q98C, I144S, S155C, S190F, V207L, S290C, Q361C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；0.9 M of potassium and sodium tartrate, 0.16 M of Lithium sulfate, 0.1 M ches
|
Resolution 3.50 Å R-free 0.272 |
| 6OE5 Splayed open prefusion RSV F captured by CR9501 and motavizumab Fabs Deposited 2019-03-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
458–484（27 aa）
|
Mutation：N67I, S215P | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；4.69 mg/mL prefusion F (PR-DM) + motavizumab Fab + CR9501 Fab, 30% (v/v) PEG400, 0.19 M ammonium sulfate, 3.1% (w/v) PEG8000, 0.1 M Tris pH 8.5
|
Resolution 4.10 Å R-free 0.306 |
| 6Z97 Structure of the prefusion SARS-CoV-2 spike glycoprotein Deposited 2020-06-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 6ZHD H11-H4 bound to Spike Deposited 2020-06-22 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 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 structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: dodecameric |
Chain I
458–484（27 aa）
Chain J
458–484（27 aa）
Chain K
458–484（27 aa）
Chain L
458–484（27 aa）
Chain M
458–484（27 aa）
Chain N
458–484（27 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 |
| 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 conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–486（29 aa）
Chain B
458–486（29 aa）
Chain C
458–486（29 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–486（29 aa）
Chain B
458–486（29 aa）
Chain C
458–486（29 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 |
| 7QUR SARS-CoV-2 Spike with ethylbenzamide-tri-iodo Siallyllactose, C3 symmetry Deposited 2022-01-18 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 7Z6V CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11 nanobody complex Deposited 2022-03-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 |
| 7Z9Q CRYO-EM STRUCTURE OF SARS-COV-2 SPIKE : H11-A10 nanobody complex Deposited 2022-03-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 |
| 7ZCE SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76 Deposited 2022-03-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 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 C
458–484（27 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 |
| 7ZH1 SARS CoV Spike protein, Closed C3 conformation Deposited 2022-04-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 2.48 Å |
| 7ZH2 SARS CoV Spike protein, Closed C1 conformation Deposited 2022-04-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | EIC LINOLEIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 27 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE-PROPANE
|
Resolution 2.71 Å |
| 7ZH5 SARS CoV Spike protein, Open conformation Deposited 2022-04-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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-PROPANE
|
Resolution 3.30 Å |
| 7ZJ6 X-31 Hemagglutinin Precursor HA0 at pH 7.5 Deposited 2022-04-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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；4s blot
|
Resolution 2.60 Å |
| 7ZJ7 X-31 Hemagglutinin Precursor HA0 at pH 4.8 Deposited 2022-04-08 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 4.8
cryo-EM vitrification conditions
Cryogen ETHANE；4s blot
|
Resolution 3.95 Å |
| 7ZJ8 X-31 Hemagglutinin Precursor HA0 at pH 7.5 after reneutralization Deposited 2022-04-08 | Different oligomeric state Different ligand/ion Different experimental conditions | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 BOG octyl beta-D-glucopyranoside × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE；4s blot
|
Resolution 3.10 Å |
| 7ZR7 OMI-42 FAB IN COMPLEX WITH SARS-COV-2 BETA SPIKE GLYCOPROTEIN Deposited 2022-05-03 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 8AJA Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein Deposited 2022-07-27 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 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 A
458–484（27 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 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 B
460–484（25 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 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 B
458–484（27 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 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 B
460–484（25 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 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 B
459–484（26 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 |
| 8BON Structure of the SARS-CoV-2 spike glycoprotein in complex with the macrocyclic peptide S1B3inL1 Deposited 2022-11-15 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 8CIM BA.2-07 FAB IN COMPLEX WITH SARS-COV-2 BA.2.12.1 SPIKE GLYCOPROTEIN Deposited 2023-02-10 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 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 conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–485（28 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain B
458–485（28 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain C
458–485（28 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 conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–485（28 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain B
458–485（28 aa）
Fragment：SARS-CoV-2 spike protein,SARS-CoV-2 spike protein
Chain C
458–485（28 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 |
| 8KG5 Prefusion RSV F Bound to Lonafarnib and D25 Fab Deposited 2023-08-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 aa）
|
Not recorded | 336 4-{2-[4-(3,10-DIBROMO-8-CHLORO-6,11-DIHYDRO-5H-BENZO[5,6]CYCLOHEPTA[1,2-B]PYRIDIN-11-YL)PIPERIDIN-1-YL]-2-OXOETHYL}PIPERIDINE-1-CARBOXAMIDE × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.17 Å |
| 8OYT Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '3 up' RBD conformation Deposited 2023-05-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 8QPR SARS-CoV-2 S protein bound to human neutralising antibody UZGENT_G5 Deposited 2023-10-03 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–485（28 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 |
| 8QTD Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab Deposited 2023-10-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 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 |
| 8R1C SD1-2 Fab in complex with SARS-CoV-2 BA.2.12.1 Spike Glycoprotein Deposited 2023-11-01 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 8R87 Cryo-EM structure of the Sars-Cov2 S trimer without RBDs Deposited 2023-11-28 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 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 |
| 8UDN A Stable Heterotrimeric Foldon with Minimum Mutation Deposited 2023-09-28 | 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
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；MPD
|
Resolution 0.97 Å R-free 0.158 |
| 8ULJ Prefusion RSV F bound by neutralizing antibody 2E08 Deposited 2023-10-16 | 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 × 12 PDB declaration: dodecameric |
Chain B
458–484（27 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；23.64%w/v PEG 1500, 0.1 M MMT buffer (DL-malic acid:MES:Tris base at a molar ratio of 1:2:2) with pH 4.36
|
Resolution 3.00 Å R-free 0.264 |
| 8ULK Prefusion RSV F bound by neutralizing antibody 1G12 Deposited 2023-10-16 | 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
458–484（27 aa）
Chain J
458–484（27 aa）
Chain K
458–484（27 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 Sodium sulfate, 20 % w/v PEG 3350
|
Resolution 4.28 Å R-free 0.279 |
| 8V5V Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation Deposited 2023-12-01 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain E
458–484（27 aa）
Chain F
458–484（27 aa）
Chain G
458–484（27 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 |
| 8YZB BA.2.86 RBD protein in complex with ACE2. Deposited 2024-04-06 | 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 A
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–481（24 aa）
Chain B
458–481（24 aa）
Chain C
458–481（24 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 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 A
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain A
458–481（24 aa）
Chain B
458–481（24 aa）
Chain C
458–481（24 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 |
| 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 conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 aa）
Chain J
458–485（28 aa）
Chain K
458–485（28 aa）
Chain L
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–485（28 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 conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain A
458–481（24 aa）
Chain B
458–481（24 aa）
Chain C
458–481（24 aa）
Chain D
458–481（24 aa）
Chain E
458–481（24 aa）
Chain F
458–481（24 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–485（28 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 |
| 8ZPP Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab Deposited 2024-05-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 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 |
| 9F9Y SARS-CoV-2 BA-2.87.1 Spike ectodomain Deposited 2024-05-09 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 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 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 C
458–484（27 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 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 C
458–484（27 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 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 C
458–484（27 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 9GDX SARS-CoV-2 Spike protein Beta Variant at 4C structural flexibility / heterogeneity analyses Deposited 2024-08-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 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 |
| 9H6U SARS-CoV-2 S protein in complex with pT1679 Fab Deposited 2024-10-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 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 |
| 9JMG Cryo-EM structure of EU-HedgehogCoV (Erinaceus/VMC/DEU/2012) S-trimer in a locked-2 conformation Deposited 2024-09-20 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 FOL FOLIC ACID × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 6
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9JMH Cryo-EM structure of HKU25-BatCoV S-trimer stabilized with 2P and x1 disulfide bond Deposited 2024-09-20 | Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Mutation：S437C,D1051C,A1052P,V1053P Mutation：S437C,D1051C,A1052P,V1053P Mutation：S437C,D1051C,A1052P,V1053P | EIC LINOLEIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 38 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9JMI Cryo-EM structure of CN-HedgehogCoV (HKU31/Erinaceus amurensis/China/2014) S-trimer in a locked-2 conformation Deposited 2024-09-20 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | FOL FOLIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9JMN Cryo-EM structure of CN-HedgehogCoV (HKU31/Erinaceus amurensis/China/2014) S-trimer in a locked-1 conformation Deposited 2024-09-20 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 25 FOL FOLIC ACID × 3 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 9JMO Cryo-EM structure of Japan-BatCoV (Vs-CoV-1) S-trimer Deposited 2024-09-20 | Different oligomeric state Different ligand/ion Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Not recorded | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 31 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.80 Å |
| 9JMP Cryo-EM structure of GD-BatCoV (BtCoV/Ii/GD/2014-422) S-trimer Deposited 2024-09-20 | Different mutation/modification Different oligomeric state Different ligand/ion | Assembly 1 Insufficient information Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
458–484（27 aa）
Chain B
458–484（27 aa）
Chain C
458–484（27 aa）
|
Mutation：A885P,S962P,A969P,N1012P,A1056P,V1057P Mutation：A885P,S962P,A969P,N1012P,A1056P,V1057P Mutation：A885P,S962P,A969P,N1012P,A1056P,V1057P | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 EIC LINOLEIC ACID × 3 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–481（24 aa）
Chain B
458–481（24 aa）
Chain C
458–481（24 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 |
| 9MKB Structure of the bacteriophage T4 portal-neck-tail complex Deposited 2024-12-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 541 PDB declaration: 541-meric |
Chain A
1–487（487 aa）
Chain B
1–487（487 aa）
Chain C
1–487（487 aa）
Chain D
1–487（487 aa）
Chain E
1–487（487 aa）
Chain F
1–487（487 aa）
Chain G
1–487（487 aa）
Chain H
1–487（487 aa）
Chain I
1–487（487 aa）
Chain J
1–487（487 aa）
Chain K
1–487（487 aa）
Chain L
1–487（487 aa）
Chain M
1–487（487 aa）
Chain N
1–487（487 aa）
Chain O
1–487（487 aa）
Chain P
1–487（487 aa）
Chain Q
1–487（487 aa）
Chain R
1–487（487 aa）
Chain S
1–487（487 aa）
Chain T
1–487（487 aa）
Chain U
1–487（487 aa）
Chain V
1–487（487 aa）
Chain W
1–487（487 aa）
Chain X
1–487（487 aa）
Chain Y
1–487（487 aa）
Chain Z
1–487（487 aa）
Chain a
1–487（487 aa）
Chain b
1–487（487 aa）
Chain c
1–487（487 aa）
Chain d
1–487（487 aa）
Chain e
1–487（487 aa）
Chain f
1–487（487 aa）
Chain g
1–487（487 aa）
Chain h
1–487（487 aa）
Chain i
1–487（487 aa）
Chain j
1–487（487 aa）
|
Not recorded | ZN ZINC ION × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Ted Pella lacey carbon 400 mesh grids
(catalog No: 01824) were used.
|
Resolution 3.80 Å |
| 9MLA Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab Deposited 2024-12-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 12 PDB declaration: 12-meric |
Chain D
459–484（26 aa）
Chain E
459–484（26 aa）
Chain F
459–484（26 aa）
|
Mutation：V498C Mutation：V498C Mutation：V498C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；Filtered and degassed
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.24 Å |
| 9MOF Structure of the bacteriophage T4 portal-neck-tail connector complex Deposited 2024-12-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 183 PDB declaration: 183-meric |
Chain A
1–487（487 aa）
Chain B
1–487（487 aa）
Chain C
1–487（487 aa）
Chain D
1–487（487 aa）
Chain E
1–487（487 aa）
Chain F
1–487（487 aa）
Chain G
1–487（487 aa）
Chain H
1–487（487 aa）
Chain I
1–487（487 aa）
Chain J
1–487（487 aa）
Chain K
1–487（487 aa）
Chain L
1–487（487 aa）
Chain M
1–487（487 aa）
Chain N
1–487（487 aa）
Chain O
1–487（487 aa）
Chain P
1–487（487 aa）
Chain Q
1–487（487 aa）
Chain R
1–487（487 aa）
Chain S
1–487（487 aa）
Chain T
1–487（487 aa）
Chain U
1–487（487 aa）
Chain V
1–487（487 aa）
Chain W
1–487（487 aa）
Chain X
1–487（487 aa）
Chain Y
1–487（487 aa）
Chain Z
1–487（487 aa）
Chain a
1–487（487 aa）
Chain b
1–487（487 aa）
Chain c
1–487（487 aa）
Chain d
1–487（487 aa）
Chain e
1–487（487 aa）
Chain f
1–487（487 aa）
Chain g
1–487（487 aa）
Chain h
1–487（487 aa）
Chain i
1–487（487 aa）
Chain j
1–487（487 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE；Ted Pella lacey carbon 400 mesh grids
(catalog No: 01824) were used.
|
Resolution 3.80 Å |
| 9O4F Pre-fusion Stabilized HERV-K Envelope Trimer Ectodomain Deposited 2025-04-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric |
Chain D
459–484（26 aa）
Chain E
459–484（26 aa）
Chain F
459–484（26 aa）
|
Mutation：V498C Mutation：V498C Mutation：V498C | NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；Filtered and degassed
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.24 Å |
| 9WDP Cyro-EM structure of prefusion RSV fusion glycoprotein in complex with Ziresovir and motavizumab Fab Deposited 2025-08-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric |
Chain A
458–485（28 aa）
Chain B
458–485（28 aa）
Chain C
458–485（28 aa）
|
Not recorded | A1EV1 ~{N}-[(3-azanyloxetan-3-yl)methyl]-2-[1,1-bis(oxidanylidene)-3,5-dihydro-2~{H}-1$l^{6},4-benzothiazepin-4-yl]-6-methyl-quinazolin-4-amine × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.27 Å |
104 other PDB entries and 107 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | WAC_BPT4 |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1290–1316； UniProt 458–484 Author chain B； PDBConstruct 1290–1316； UniProt 458–484 Author chain C； PDBConstruct 1290–1316； UniProt 458–484 |
