← Back to search
8jag

Cryo-EM structure of SARS-CoV-1 RBD in complex with W328-6H2 (local refinement)

Method: ELECTRON MICROSCOPY Dmax: 184.1 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Spike glycoprotein

Severe acute respiratory syndrome-related 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 A； UniProt 1–1255 Not recorded H chain of 6H2 Fab region × 1 L chain of 6H2 Fab region × 1 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

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 8JAG 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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
2DD8 Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody Deposited 2006-01-24 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 S 317–518（202 aa） Fragment：RECEPTOR-BINDING DOMAIN, residues 317-518
Not recorded 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
2DD8 Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing Antibody Deposited 2006-01-24 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain S 317–518（202 aa） Fragment：RECEPTOR-BINDING DOMAIN, residues 317-518
Not recorded 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
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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 method 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 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 method 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 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 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 method 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 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 method 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 method 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 method 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 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 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 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 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 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 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 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 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 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 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 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 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 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
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 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 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 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 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 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 method 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 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 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 98 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPIKE_SARS
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1255； UniProt 1–1255

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 8jag

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8jag
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8jag
Deposition date deposition_date2023-05-06
Structure title titleCryo-EM structure of SARS-CoV-1 RBD in complex with W328-6H2 (local refinement)
Keywords keywordsCryo-EM, Complex, SARS-CoV-1, antibody, Homo sapiens, IgG, RBD, local refinement, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.59 Å
Radius of gyration Rg (electron density) rg_electron51.08 Å
Forward intensity I(0) i0277183000.00
Molecular weight molecular_weight138670.0 kDa
Excluded volume excluded_volume174030 ų
Envelope volume envelope_volume276220 ų
Hydration-shell volume shell_volume49036 ų
Envelope diameter envelope_diameter181.9 Å
Shell Rg shell_rg48.77 Å
Envelope Rg envelope_rg49.84 Å
Shape Rg shape_rg51.10 Å
Total Rg total_rg50.90 Å
Total atoms total_atoms9772
Residues n_residues1244
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax184.1 Å
Rg (real space) rg_real50.89 Å
Rg uncertainty (real space) rg_real_error2.68 Å
I(0) (real space) i0_real2.7720e+08
I(0) uncertainty (real space) i0_real_error5.9000e+06
Rg (reciprocal space) rg_reciprocal50.33 Å
I(0) (reciprocal space) i0_reciprocal277000000.0000
Solution quality estimate total_estimate0.8335
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary53.5 Å
Skewness Skewness skewness0.465
Kurtosis Kurtosis kurtosis-0.279
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10200000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.768; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.759; Smooth: 0.771
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▶

8. Citations (1)

▶

9. Files and Curves (10)