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2dd8

Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody

Method: X-RAY DIFFRACTION Dmax: 105.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

IGG Heavy Chain

Homo sapiens

UniProt Q6PJF1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain H； UniProt 20–256 Fragment：Fab m396, Heavy Chain IGG Light Chain × 1 （Q8N355） Spike glycoprotein × 1 （P59594） PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.261
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain H； UniProt 20–256 Fragment：Fab m396, Heavy Chain IGG Light Chain × 1 （Q8N355） Spike glycoprotein × 1 （P59594） PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.261

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 2DD8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RHH Crystal Structure of the Broadly HIV-1 Neutralizing Fab X5 at 1.90 Angstrom Resolution Deposited 2003-11-14 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 25–256（232 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；PEG400, HEPES, 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.90 Å R-free 0.227
1RHH Crystal Structure of the Broadly HIV-1 Neutralizing Fab X5 at 1.90 Angstrom Resolution Deposited 2003-11-14 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 25–256（232 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；PEG400, HEPES, 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Resolution 1.90 Å R-free 0.227
2QL1 Structural Characterization of a Mutated, ADCC-Enhanced Human Fc Fragment Deposited 2007-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 256–480（225 aa） Fragment：Antibody Fc fragment
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；8% PEG 3350, 200 mM Zn Acetate, 5% Glycerol, 0.1 M Imidazole -Malate buffer, pH 8.0, VAPOR DIFFUSION, temperature 298.0K
Resolution 2.53 Å R-free 0.293
3C2S Structural Characterization of a Human Fc Fragment Engineered for Lack of Effector Functions Deposited 2008-01-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 256–480（225 aa） Fragment：ANTIBODY FC FRAGMENT, residues 256-480
Mutation：L234F, L234E,P331S ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；5% PEG 3350, 200 mM Zn Acetate, 0.1 M Imidazole Malate, 5% Glycerol, pH 8.0, VAPOR DIFFUSION, temperature 298.0K
Resolution 2.30 Å R-free 0.275

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6PJF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain H； PDBConstruct 1–224； UniProt 20–256

IGG Light Chain

Homo sapiens

UniProt Q8N355

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain L； UniProt 20–234 Fragment：Fab m396, Light Chain IGG Heavy Chain × 1 （Q6PJF1） Spike glycoprotein × 1 （P59594） PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.261
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain L； UniProt 20–234 Fragment：Fab m396, Light Chain IGG Heavy Chain × 1 （Q6PJF1） Spike glycoprotein × 1 （P59594） PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.261

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 2DD8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5UGY Influenza hemagglutinin in complex with a neutralizing antibody Deposited 2017-01-10 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 L 119–231（113 aa） Fragment：Fab
Chain M 119–231（113 aa） Fragment：Fab
Chain N 119–231（113 aa） Fragment：Fab
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；2.2 M ammonium sulfate, 100 mM Tris, 5% PEG400, pH 7.5
Resolution 2.80 Å R-free 0.289
6DC3 RSV prefusion F bound to RSD5 Fab Deposited 2018-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 117–234（118 aa）
Not recorded SO4 SULFATE ION × 13 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.8 M Lithium sulfate, 0.1 M Tris pH 8.0
Resolution 3.50 Å R-free 0.205
6UDJ HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074 Deposited 2019-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 125–234（110 aa）
Chain L 125–234（110 aa）
Chain R 125–234（110 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；0 blot force, 3.0 second blot time, 3 uL sample added to freshly glow discharged grids
Resolution 2.50 Å
6UDK HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074 Deposited 2019-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric
Chain B 125–234（110 aa）
Chain I 125–234（110 aa）
Chain P 125–234（110 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；0 blot force, 3.5 second blot time, 3 uL sample added to freshly glow-discharged grids
Resolution 3.90 Å
6VPY I33M (I3.2 mutant from CH103 Lineage) Deposited 2020-02-04 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 126–234（109 aa） Fragment：FAB,FAB
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5 M ammonium sulfate, 100 mM HEPES, pH 7.23, 5% PEG400
Resolution 2.36 Å R-free 0.223
6VPY I33M (I3.2 mutant from CH103 Lineage) Deposited 2020-02-04 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 L 126–234（109 aa） Fragment：FAB,FAB
Not recorded GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5 M ammonium sulfate, 100 mM HEPES, pH 7.23, 5% PEG400
Resolution 2.36 Å R-free 0.223

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8N355_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain L； PDBConstruct 1–213； UniProt 20–234

Spike glycoprotein

SARS coronavirus

UniProt P59594

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain S； UniProt 317–518 Fragment：RECEPTOR-BINDING DOMAIN, residues 317-518 IGG Heavy Chain × 1 （Q6PJF1） IGG Light Chain × 1 （Q8N355） PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.261
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain S； UniProt 317–518 Fragment：RECEPTOR-BINDING DOMAIN, residues 317-518 IGG Heavy Chain × 1 （Q6PJF1） IGG Light Chain × 1 （Q8N355） PO4 PHOSPHATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；15v/v% Glycerol, 20% PEG 6000, 100mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.30 Å R-free 0.261

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 2DD8 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WNC Crystal structure of the SARS-CoV Spike protein fusion core Deposited 2004-07-29 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 900–948（49 aa） Fragment：residues 900-1184
Chain A 1144–1185（42 aa） Fragment：residues 900-1184
Chain B 900–948（49 aa） Fragment：residues 900-1184
Chain B 1144–1185（42 aa） Fragment：residues 900-1184
Chain C 900–948（49 aa） Fragment：residues 900-1184
Chain C 1144–1185（42 aa） Fragment：residues 900-1184
Chain D 900–948（49 aa） Fragment：residues 900-1184
Chain D 1144–1185（42 aa） Fragment：residues 900-1184
Chain E 900–948（49 aa） Fragment：residues 900-1184
Chain E 1144–1185（42 aa） Fragment：residues 900-1184
Chain F 900–948（49 aa） Fragment：residues 900-1184
Chain F 1144–1185（42 aa） Fragment：residues 900-1184
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；291 K；PEG4000, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.273
1WNC Crystal structure of the SARS-CoV Spike protein fusion core Deposited 2004-07-29 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 A 900–948（49 aa） Fragment：residues 900-1184
Chain A 1144–1185（42 aa） Fragment：residues 900-1184
Chain B 900–948（49 aa） Fragment：residues 900-1184
Chain B 1144–1185（42 aa） Fragment：residues 900-1184
Chain C 900–948（49 aa） Fragment：residues 900-1184
Chain C 1144–1185（42 aa） Fragment：residues 900-1184
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；291 K；PEG4000, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.273
1WNC Crystal structure of the SARS-CoV Spike protein fusion core Deposited 2004-07-29 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 D 900–948（49 aa） Fragment：residues 900-1184
Chain D 1144–1185（42 aa） Fragment：residues 900-1184
Chain E 900–948（49 aa） Fragment：residues 900-1184
Chain E 1144–1185（42 aa） Fragment：residues 900-1184
Chain F 900–948（49 aa） Fragment：residues 900-1184
Chain F 1144–1185（42 aa） Fragment：residues 900-1184
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；291 K；PEG4000, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.80 Å R-free 0.273
1WYY Post-fusion hairpin conformation of the sars coronavirus spike glycoprotein Deposited 2005-02-18 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 885–981（97 aa） Fragment：residues 885-1189
Chain A 1145–1189（45 aa） Fragment：residues 885-1189
Not recorded CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 8000, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.20 Å R-free 0.249
1WYY Post-fusion hairpin conformation of the sars coronavirus spike glycoprotein Deposited 2005-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 885–981（97 aa） Fragment：residues 885-1189
Chain B 1145–1189（45 aa） Fragment：residues 885-1189
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 8000, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.20 Å R-free 0.249
1WYY Post-fusion hairpin conformation of the sars coronavirus spike glycoprotein Deposited 2005-02-18 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 B 885–981（97 aa） Fragment：residues 885-1189
Chain B 1145–1189（45 aa） Fragment：residues 885-1189
Not recorded CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；PEG 8000, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.20 Å R-free 0.249
1ZV7 A structure-based mechanism of SARS virus membrane fusion Deposited 2005-06-01 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 1150–1193（44 aa） Fragment：residues 1150-1193
Chain B 1150–1193（44 aa） Fragment：residues 1150-1193
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG MME 2000, Nickel chloride, Tris-HCL, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.258
1ZV8 A structure-based mechanism of SARS virus membrane fusion Deposited 2005-06-01 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 901–950（50 aa） Fragment：residues 901-950
Chain B 1150–1185（36 aa） Fragment：residues 1150-1185
Chain C 901–950（50 aa） Fragment：residues 901-950
Chain D 1150–1185（36 aa） Fragment：residues 1150-1185
Chain E 901–950（50 aa） Fragment：residues 901-950
Chain F 1150–1185（36 aa） Fragment：residues 1150-1185
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；PEG 8000, zinc acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.94 Å R-free 0.274
1ZV8 A structure-based mechanism of SARS virus membrane fusion Deposited 2005-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain G 901–950（50 aa） Fragment：residues 901-950
Chain H 1150–1185（36 aa） Fragment：residues 1150-1185
Chain I 901–950（50 aa） Fragment：residues 901-950
Chain J 1150–1185（36 aa） Fragment：residues 1150-1185
Chain K 901–950（50 aa） Fragment：residues 901-950
Chain L 1150–1185（36 aa） Fragment：residues 1150-1185
Not recorded NA SODIUM ION × 4 CAC CACODYLATE ION × 1 ZN ZINC ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；PEG 8000, zinc acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.94 Å R-free 0.274
1ZVA A structure-based mechanism of SARS virus membrane fusion Deposited 2005-06-01 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 926–962（37 aa） Fragment：residues 926-962 and residues 1150-1183
Chain A 1150–1183（34 aa） Fragment：residues 926-962 and residues 1150-1183
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；PEG 1500, sodium formate, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.50 Å R-free 0.246
1ZVB A structure-based mechanism of SARS virus membrane fusion Deposited 2005-06-01 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 940–973（34 aa） Fragment：residues 940-973
Chain B 940–973（34 aa） Fragment：residues 940-973
Chain C 940–973（34 aa） Fragment：residues 940-973
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；PEG 4000, isopropanol, sodium citrate, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.239
2AJF Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor Deposited 2005-08-01 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 323–502（180 aa） Fragment：receptor-binding domain, residues 323-502
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；100 mM Tris pH 8.2, 24% PEG6000, 150 mM NaCl, 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, pH 7.5, pH 7.50
Resolution 2.90 Å R-free 0.275
2AJF Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor Deposited 2005-08-01 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 323–502（180 aa） Fragment：receptor-binding domain, residues 323-502
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；100 mM Tris pH 8.2, 24% PEG6000, 150 mM NaCl, 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, pH 7.5, pH 7.50
Resolution 2.90 Å R-free 0.275
2BEQ Structure of a Proteolytically Resistant Core from the Severe Acute Respiratory Syndrome Coronavirus S2 Fusion Protein Deposited 2004-11-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric
Chain A 914–949（36 aa） Fragment：RESIDUES 914-949
Chain B 914–949（36 aa） Fragment：RESIDUES 914-949
Chain C 914–949（36 aa） Fragment：RESIDUES 914-949
Chain D 1148–1193（46 aa） Fragment：RESIDUES 1148-1193
Chain E 1148–1193（46 aa） Fragment：RESIDUES 1148-1193
Chain F 1148–1193（46 aa） Fragment：RESIDUES 1148-1193
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) 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 pH 6.5；30% PEG8K, PH 7.0 100MM SODIUM CACODYLATE PH 6.5, 200MM SODIUM ACETATE
Resolution 1.60 Å R-free 0.241
2BEZ Structure of a proteolitically resistant core from the severe acute respiratory syndrome coronavirus S2 fusion protein Deposited 2004-12-02 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 C 896–972（77 aa） Fragment：RESIDUES 896-972
Chain F 1142–1183（42 aa） Fragment：RESIDUES 1142-1183
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；0.1M TRIS-HCL, PH 7.0, 1.8M AMMONIUM SULPHATE, 0.1M NACL
Resolution 1.60 Å R-free 0.244
2FXP Solution Structure of the SARS-Coronavirus HR2 Domain Deposited 2006-02-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1140–1193（54 aa） Fragment：HR2 domain, residues 1140-1193
Chain B 1140–1193（54 aa） Fragment：HR2 domain, residues 1140-1193
Chain C 1140–1193（54 aa） Fragment：HR2 domain, residues 1140-1193
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 10 mM；Pressure ambient
NMR sample composition 1 mM monomer, 10 mM PO4, pH 7.0, 30% TFE
Resolution not provided
2GHV Crystal structure of SARS spike protein receptor binding domain Deposited 2006-03-27 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 C 317–512（196 aa） Fragment：RBD of spike protein S1 (318-510)
Chain E 317–512（196 aa） Fragment：RBD of spike protein S1 (318-510)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；290 K；4% PEG4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.20 Å R-free 0.213
2GHW Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R Deposited 2006-03-27 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 A 317–510（194 aa） Fragment：RBD of spike protein S1 (318-510)
Not recorded CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；290 K；12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.30 Å R-free 0.295
2GHW Crystal structure of SARS spike protein receptor binding domain in complex with a neutralizing antibody, 80R Deposited 2006-03-27 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 C 317–510（194 aa） Fragment：RBD of spike protein S1 (318-510)
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；290 K；12.5% PEG4000, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 2.30 Å R-free 0.295
2RUM Solution structure of Fusion peptide Deposited 2014-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 770–788（19 aa）
Mutation：Y2W No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.7；315 K
NMR sample composition 125 mM [U-99% 2H] DPC-1, 0.5 mM Fusion Peptide-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2RUN Solution Structure of Pre Transmembrane domain Deposited 2014-11-06 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 1185–1202（18 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.7；315 K
NMR sample composition 0.5 mM Pre transmembrane domain-1, 125 mM [U-99% 2H] DPC-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2RUO Solution Structure of Internal Fusion Peptide Deposited 2014-11-06 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 873–888（16 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4.7；315 K
NMR sample composition 0.5 mM Internal fusion peptide-1, 125 mM [U-99% 2H] DPC-2, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3BGF X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab Deposited 2007-11-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 318–510（193 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M MES, 14% PEG 20000, 10-15% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.286
3BGF X-ray crystal structure of the SARS coronavirus spike receptor binding domain in complex with F26G19 Fab Deposited 2007-11-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain S 318–510（193 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1 M MES, 14% PEG 20000, 10-15% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.286
3D0G Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus human strain complexed with human-civet chimeric receptor ACE2 Deposited 2008-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 324–502（179 aa） Fragment：residues 324-502
Chain F 324–502（179 aa） Fragment：residues 324-502
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 5 ZN ZINC ION × 2 CL CHLORIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Resolution 2.80 Å R-free 0.279
3D0H Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2008-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 324–502（179 aa） Fragment：residues 324-502
Chain F 324–502（179 aa） Fragment：residues 324-502
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 5 ZN ZINC ION × 2 CL CHLORIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Resolution 3.10 Å R-free 0.302
3D0H Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2008-05-01 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 E 324–502（179 aa） Fragment：residues 324-502
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 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；pH 8.5；298 K；100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Resolution 3.10 Å R-free 0.302
3D0H Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2008-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 324–502（179 aa） Fragment：residues 324-502
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4 ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Resolution 3.10 Å R-free 0.302
3D0I Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2008-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 324–502（179 aa） Fragment：residues 324-502
Chain F 324–502（179 aa） Fragment：residues 324-502
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 5 ZN ZINC ION × 2 CL CHLORIDE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Resolution 2.90 Å R-free 0.278
3D0I Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2008-05-01 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 E 324–502（179 aa） Fragment：residues 324-502
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 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；pH 8.5；298 K；100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Resolution 2.90 Å R-free 0.278
3D0I Crystal structure of spike protein receptor-binding domain from the 2005-2006 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2008-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 324–502（179 aa） Fragment：residues 324-502
Not recorded NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 4 ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；298 K；100 mM Tris, 22% PEG6000, 100 mM NaCl, pH 8.5, vapor diffusion, temperature 298K
Resolution 2.90 Å R-free 0.278
3SCI Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus human strain complexed with human receptor ACE2 Deposited 2011-06-07 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 E 306–527（222 aa） Fragment：receptor binding domain (UNP residues 306-527)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 2.90 Å R-free 0.283
3SCI Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus human strain complexed with human receptor ACE2 Deposited 2011-06-07 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 F 306–527（222 aa） Fragment：receptor binding domain (UNP residues 306-527)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 2.90 Å R-free 0.283
3SCJ Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human receptor ACE2 Deposited 2011-06-07 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 E 323–502（180 aa） Fragment：receptor binding domain (UNP residues 323-502)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 3.00 Å R-free 0.278
3SCJ Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human receptor ACE2 Deposited 2011-06-07 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 F 323–502（180 aa） Fragment：receptor binding domain (UNP residues 323-502)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 3.00 Å R-free 0.278
3SCK Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2011-06-07 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 324–502（179 aa） Fragment：receptor binding domain (UNP residues 324-502)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；20 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 3.00 Å R-free 0.285
3SCK Crystal structure of spike protein receptor-binding domain from a predicted SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2 Deposited 2011-06-07 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 324–502（179 aa） Fragment：receptor binding domain (UNP residues 324-502)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；20 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 3.00 Å R-free 0.285
3SCL Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic strain complexed with human-civet chimeric receptor ACE2 Deposited 2011-06-07 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 324–502（179 aa） Fragment：receptor binding domain (UNP residues 324-502)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 3.00 Å R-free 0.292
3SCL Crystal structure of spike protein receptor-binding domain from SARS coronavirus epidemic strain complexed with human-civet chimeric receptor ACE2 Deposited 2011-06-07 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 324–502（179 aa） Fragment：receptor binding domain (UNP residues 324-502)
Not recorded ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；295 K；100 mM Tris, pH 8.5, 20% PEG6000, 100 mM sodium chloride, EVAPORATION, temperature 295K
Resolution 3.00 Å R-free 0.292
5WRG SARS-CoV spike glycoprotein Deposited 2016-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–1196（1196 aa） Fragment：UNP RESIDUES 1-1196
Chain B 1–1196（1196 aa） Fragment：UNP RESIDUES 1-1196
Chain C 1–1196（1196 aa） Fragment：UNP RESIDUES 1-1196
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
5X4S Structure of the N-terminal domain (NTD)of SARS-CoV spike protein Deposited 2017-02-14 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 14–292（279 aa） Fragment：UNP residues 14-292
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；1.3 M Na/K hydrogen phosphate
Resolution 2.20 Å R-free 0.282
5XJK NMR Structure and Localization of a Large Fragment of the SARS-CoV Fusion Protein: Implications in Viral Cell Fusion Deposited 2017-05-02 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 758–821（64 aa） Fragment：UNP RESIDUES 758-821
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1
NMR sample composition 0.2 M [U-13C; U-15N] Large Fragment of the SARS-CoV Fusion Protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
5XLR Structure of SARS-CoV spike glycoprotein Deposited 2017-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–1196（1196 aa）
Chain B 1–1196（1196 aa）
Chain C 1–1196（1196 aa）
Mutation：R667A Mutation：R667A Mutation：R667A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
5ZVM Crystal Structure of the Human Coronavirus SARS HR1 motif in complex with pan-CoVs inhibitor EK1 Deposited 2018-05-11 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 892–970（79 aa） Fragment：UNP residues 892-970
Chain B 892–970（79 aa） Fragment：UNP residues 892-970
Chain C 892–970（79 aa） Fragment：UNP residues 892-970
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；0.2M Li2SO4, 0.1M BIS-Tris, pH 5.5, 25% PEG3350
Resolution 3.30 Å R-free 0.301
6ACC Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-free conformation with three RBD in down conformation Deposited 2018-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–1196（1196 aa）
Chain B 1–1196（1196 aa）
Chain C 1–1196（1196 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6ACD Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-free conformation with one RBD in up conformation Deposited 2018-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–1196（1196 aa）
Chain B 1–1196（1196 aa）
Chain C 1–1196（1196 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6ACG Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 1 Deposited 2018-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1196（1196 aa）
Chain B 1–1196（1196 aa）
Chain C 1–1196（1196 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
6ACJ Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 2 Deposited 2018-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1196（1196 aa）
Chain B 1–1196（1196 aa）
Chain C 1–1196（1196 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6ACK Trypsin-cleaved and low pH-treated SARS-CoV spike glycoprotein and ACE2 complex, ACE2-bound conformation 3 Deposited 2018-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1196（1196 aa）
Chain B 1–1196（1196 aa）
Chain C 1–1196（1196 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6CRV SARS Spike Glycoprotein, Stabilized variant, C3 symmetry Deposited 2018-03-19 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 14–1190（1177 aa）
Chain B 14–1190（1177 aa）
Chain C 14–1190（1177 aa）
Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6CRW SARS Spike Glycoprotein, Stabilized variant, single upwards S1 CTD conformation Deposited 2018-03-19 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 14–1190（1177 aa）
Chain B 14–1190（1177 aa）
Chain C 14–1190（1177 aa）
Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6CRX SARS Spike Glycoprotein, Stabilized variant, two S1 CTDs in the upwards conformation Deposited 2018-03-19 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 14–1190（1177 aa）
Chain B 14–1190（1177 aa）
Chain C 14–1190（1177 aa）
Mutation：K968P, V968P Mutation：K968P, V968P Mutation：K968P, V968P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6CRZ SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, C3 symmetry Deposited 2018-03-19 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 14–1190（1177 aa）
Chain B 14–1190（1177 aa）
Chain C 14–1190（1177 aa）
Mutation：K968P, V968P Mutation：K968P, V968P Mutation：K968P, V968P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
6CS0 SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, one S1 CTD in an upwards conformation Deposited 2018-03-19 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 14–1190（1177 aa）
Chain B 14–1190（1177 aa）
Chain C 14–1190（1177 aa）
Mutation：K968P, V968P Mutation：K968P, V968P Mutation：K968P, V968P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6CS1 SARS Spike Glycoprotein, Trypsin-cleaved, Stabilized variant, two S1 CTDs in an upwards conformation Deposited 2018-03-19 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 14–1190（1177 aa）
Chain B 14–1190（1177 aa）
Chain C 14–1190（1177 aa）
Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
6CS2 SARS Spike Glycoprotein - human ACE2 complex, Stabilized variant, all ACE2-bound particles Deposited 2018-03-19 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 × 4 PDB declaration: tetrameric
Chain A 14–1190（1177 aa）
Chain B 14–1190（1177 aa）
Chain C 14–1190（1177 aa）
Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6M3W Post-fusion structure of SARS-CoV spike glycoprotein Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 688–1178（491 aa）
Chain B 688–1178（491 aa）
Chain C 688–1178（491 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 3.90 Å
6NB6 SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 1) Deposited 2018-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 14–1193（1180 aa）
Chain B 14–1193（1180 aa）
Chain C 14–1193（1180 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 17 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
6NB7 SARS-CoV complex with human neutralizing S230 antibody Fab fragment (state 2) Deposited 2018-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 14–1193（1180 aa）
Chain B 14–1193（1180 aa）
Chain C 14–1193（1180 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 4.50 Å
6VW1 Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 Deposited 2020-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 306–441（136 aa）
Chain E 505–521（17 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 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 306–441（136 aa）
Chain F 505–521（17 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
6WAQ Crystal structure of the SARS-CoV-1 RBD bound by the cross-reactive single-domain antibody SARS VHH-72 Deposited 2020-03-25 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 B 320–502（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris pH 8.5, 0.2 M LiSO4, 0.1 M LiCl, 8% PEG 8000
Resolution 2.20 Å R-free 0.236
6WAQ Crystal structure of the SARS-CoV-1 RBD bound by the cross-reactive single-domain antibody SARS VHH-72 Deposited 2020-03-25 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 D 320–502（183 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris pH 8.5, 0.2 M LiSO4, 0.1 M LiCl, 8% PEG 8000
Resolution 2.20 Å R-free 0.236
7FC6 Crystal structure of SARS-CoV 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 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain S 321–512（192 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；0.03M Citric acid/0.07M BIS-TRIS propane pH7.6, 20% w/v polyethylene glycol 3350
Resolution 2.65 Å R-free 0.235
7RKS Structure of the SARS-CoV receptor binding domain in complex with the human neutralizing antibody Fab fragment, C118 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 R 321–510（190 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M sodium fluoride, 20% PEG 3,350
Resolution 2.70 Å R-free 0.247
7RKS Structure of the SARS-CoV receptor binding domain in complex with the human neutralizing antibody Fab fragment, C118 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 S 321–510（190 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2M sodium fluoride, 20% PEG 3,350
Resolution 2.70 Å R-free 0.247
7SG4 Structure of SARS-CoV S protein in complex with Receptor Binding Domain antibody DH1047 Deposited 2021-10-04 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 × 5 PDB declaration: pentameric
Chain A 1–1190（1190 aa）
Chain B 1–1190（1190 aa）
Chain C 1–1190（1190 aa）
Mutation：K968P, V969P Mutation：K968P, V969P Mutation：K968P, V969P NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 47 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.43 Å
7WR9 Local CryoEM structure of the SARS-CoV S2P 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 F 323–502（180 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 3.24 Å
7WSF Cryo-EM structure of SARS-CoV spike receptor-binding domain in complex with 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 321–502（182 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
7WSG Cryo-EM structure of SARS-CoV 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 321–502（182 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
7X2J Crystal structure of nanobody Nb70 with SARS-CoV 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 × 2 PDB declaration: dimeric
Chain S 306–516（211 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；291.15 K；0.2M Ammonium sulfate, 0.1M Bis-Tris pH 4.4, 21% w/v Polyethylene glycol 3350
Resolution 2.40 Å R-free 0.235
7X7V Cryo-EM structure of SARS-CoV 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 Other combination Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 320–508（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 3.83 Å
7Y3N Crystal structure of SARS-CoV 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 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 306–527（222 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 5.9；291 K；20% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.9, 20% w/v Polyethylene glycol 4000
Resolution 2.97 Å R-free 0.263
7Y3N Crystal structure of SARS-CoV receptor binding domain in complex with human antibody BIOLS56 Deposited 2022-06-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 306–527（222 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 5.9；291 K；20% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.9, 20% w/v Polyethylene glycol 4000
Resolution 2.97 Å R-free 0.263
7Y3N Crystal structure of SARS-CoV receptor binding domain in complex with human antibody BIOLS56 Deposited 2022-06-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 306–527（222 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 5.9；291 K；20% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.9, 20% w/v Polyethylene glycol 4000
Resolution 2.97 Å R-free 0.263
7ZH1 SARS CoV Spike protein, Closed C3 conformation Deposited 2022-04-05 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 Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 14–1193（1180 aa）
Chain B 14–1193（1180 aa）
Chain C 14–1193（1180 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 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 14–1193（1180 aa）
Chain B 14–1193（1180 aa）
Chain C 14–1193（1180 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 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 14–1193（1180 aa）
Chain B 14–1193（1180 aa）
Chain C 14–1193（1180 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
8H0X Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-1 Conformation Deposited 2022-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Mutation：S370C, D967C Mutation：S370C, D967C Mutation：S370C, D967C EIC LINOLEIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 BLA BILIVERDINE IX ALPHA × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8H0Y Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-112 Conformation Deposited 2022-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Not recorded EIC LINOLEIC ACID × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 46 BLA BILIVERDINE IX ALPHA × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8H0Z Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-122 Conformation Deposited 2022-09-30 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 Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Mutation：S370C, D967C Mutation：S370C, D967C Mutation：S370C, D967C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 BLA BILIVERDINE IX ALPHA × 3 EIC LINOLEIC ACID × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
8H10 Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Locked-2 Conformation Deposited 2022-09-30 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 Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Mutation：S370C, D967C Mutation：S370C, D967C Mutation：S370C, D967C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 BLA BILIVERDINE IX ALPHA × 3 EIC LINOLEIC ACID × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
8H11 Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Closed Conformation Deposited 2022-09-30 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 Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Mutation：S370C, D967C Mutation：S370C, D967C Mutation：S370C, D967C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 37 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.72 Å
8H12 Structure of SARS-CoV-1 Spike Protein with Engineered x2 Disulfide (G400C and V969C), Locked-2 Conformation Deposited 2022-09-30 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 Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Mutation：G400C, V969C Mutation：G400C, V969C Mutation：G400C, V969C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 39 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.45 Å
8H13 Structure of SARS-CoV-1 Spike Protein with Engineered x2 Disulfide (G400C and V969C), Closed Conformation Deposited 2022-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Mutation：G400C, V969C Mutation：G400C, V969C Mutation：G400C, V969C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
8H14 Structure of SARS-CoV-1 Spike Protein with Engineered x3 Disulfide (D414C and V969C), Locked-1 Conformation Deposited 2022-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Mutation：D414C and V969C Mutation：D414C and V969C Mutation：D414C and V969C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 42 EIC LINOLEIC ACID × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8H15 Structure of SARS-CoV-1 Spike Protein (S/native) at pH 5.5, Closed Conformation Deposited 2022-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 5.54；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.14 Å
8H16 Structure of SARS-CoV-1 Spike Protein (S/native) at pH 5.5, Open Conformation Deposited 2022-09-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 15–1193（1179 aa）
Chain B 15–1193（1179 aa）
Chain C 15–1193（1179 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 32 ELECTRON MICROSCOPY
cryo-EM buffer pH 5.54；Gibco PBS C10010
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
8JAG Cryo-EM structure of SARS-CoV-1 RBD in complex with W328-6H2 (local refinement) Deposited 2023-05-06 Different construct 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 1–1255（1255 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 3.55 Å
8KDM Structure of SARS-CoV Spike protein complexed with antibody PW5-5 Deposited 2023-08-09 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 1–1190（1190 aa）
Chain B 1–1190（1190 aa）
Chain C 1–1190（1190 aa）
Mutation：S577A, K968P, V969P Mutation：S577A, K968P, V969P Mutation：S577A, K968P, V969P No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
8KDS Trimer state of SARS-CoV 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 × 9 PDB declaration: nonameric
Chain A 1–1190（1190 aa）
Chain B 1–1190（1190 aa）
Chain C 1–1190（1190 aa）
Mutation：S577A, K968P, V969P Mutation：S577A, K968P, V969P Mutation：S577A, K968P, V969P No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8KDT The local refined map of SARS-CoV Spike protein complexed with antibody PW5-5 Deposited 2023-08-10 Different construct Different mutation/modification 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 1–1190（1190 aa）
Mutation：S577A, K968P, V969P No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.04 Å
8KEK Monomer state of SARS-CoV Spike protein complexed with antibody PW5-535 Deposited 2023-08-11 Different construct Different mutation/modification 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 1–1190（1190 aa）
Mutation：K968P, V969P, S577A No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
8VPF Structure of SARS-CoV spike in complex with CoV1-65 Fab (NTD-bound) Deposited 2024-01-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–1190（1190 aa）
Chain B 1–1190（1190 aa）
Chain C 1–1190（1190 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 15 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；1X TBS
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8WCG Crystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347 Deposited 2023-09-12 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 320–516（197 aa）
Chain B 320–516（197 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；20% w/v PEG4000, 0.1 M Tris 8.0
Resolution 2.60 Å R-free 0.279
8WOZ Cryo-EM structure of SARS-CoV RBD in complex with rabbit ACE2 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 306–527（222 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
8XZB The structure of fox ACE2 and SARS-CoV 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 C 306–527（222 aa） Fragment：RBD
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å

76 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPIKE_CVHSA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain S； PDBConstruct 1–202； UniProt 317–518

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2dd8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2dd8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2dd8
Deposition date deposition_date2006-01-24
Structure title titleCrystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody
Keywords keywordsSARS, S protein, antibody, epitopes, vaccines, inhibitors, IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX; IMMUNE SYSTEM/VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.54 Å
Radius of gyration Rg (electron density) rg_electron31.52 Å
Forward intensity I(0) i074709000.00
Molecular weight molecular_weight67627.0 kDa
Excluded volume excluded_volume84217 ų
Envelope volume envelope_volume110480 ų
Hydration-shell volume shell_volume31497 ų
Envelope diameter envelope_diameter112.6 Å
Shell Rg shell_rg35.99 Å
Envelope Rg envelope_rg31.58 Å
Shape Rg shape_rg31.47 Å
Total Rg total_rg32.07 Å
Total atoms total_atoms4759
Residues n_residues618
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax105.7 Å
Rg (real space) rg_real31.86 Å
Rg uncertainty (real space) rg_real_error1.05 Å
I(0) (real space) i0_real7.4710e+07
I(0) uncertainty (real space) i0_real_error1.2750e+06
Rg (reciprocal space) rg_reciprocal31.73 Å
I(0) (reciprocal space) i0_reciprocal74700000.0000
Solution quality estimate total_estimate0.8398
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.7 Å
Skewness Skewness skewness0.572
Kurtosis Kurtosis kurtosis-0.231
Angular range angular_range— – 0.2500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8839000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.797; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.886; Smooth: 0.638
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2dd8h1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2dd8h2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2dd8h3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2dd8l1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd2dd8l2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd2dd8s1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.318 — SARS receptor-binding domain-like
Superfamily Superfamily superfamilyd.318.1 — SARS receptor-binding domain-like
Family Family familyd.318.1.1 — SARS receptor-binding domain-like

CATH v4.4 (5 domains)

Domain ID domain_id2dd8H01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2dd8H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2dd8L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2dd8L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2dd8S01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1840 — Spike protein, C-terminal core receptor binding subdomain
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8. Citations (1)

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9. Files and Curves (10)