7VMU

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

• PDB DOI: https://doi.org/10.2210/pdb7VMU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli, Baculovirus expression vector pFastBac1-HM
• Mutation(s): No 


• Deposited: 2021-10-09 Released: 2021-11-03 
• Deposition Author(s): Guo, Y., Wang, W., Jiao, P., Yang, H., Rao, Z., Cheng, G.
• Funding Organization(s): Other government, National Natural Science Foundation of China (NSFC), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.273 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 

Literature

Antibody engineering improves neutralization activity against K417 spike mutant SARS-CoV-2 variants.

Li, L., Gao, M., Jiao, P., Zu, S., Deng, Y.Q., Wan, D., Cao, Y., Duan, J., Aliyari, S.R., Li, J., Shi, Y., Rao, Z., Qin, C.F., Guo, Y., Cheng, G., Yang, H.

(2022) Cell Biosci 12: 63-63

• PubMed: 35581593 
• DOI: https://doi.org/10.1186/s13578-022-00794-7
• Primary Citation of Related Structures:  
  7VMU


• PubMed Abstract: 
  

  Neutralizing antibodies are approved drugs to treat coronavirus disease-2019 (COVID-19) patients, yet mutations in severe acute respiratory syndrome coronavirus (SARS-CoV-2) variants may reduce the antibody neutralizing activity. New monoclonal antibodies (mAbs) and antibody remolding strategies are recalled in the battle with COVID-19 epidemic.

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Organizational Affiliation: 

Institute of Systems Medicine, Chinese Academy of Medical Science & Peking Union College, Beijing, 100005, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.89 kDa 
• Atom Count: 3,064 
• Modelled Residue Count: 396 
• Deposited Residue Count: 426 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv E4	A	245	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	181	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.273 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.021	α = 90
b = 97.021	β = 90
c = 93.244	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-03 
Deposition Author(s): Guo, Y., Wang, W., Jiao, P., Yang, H., Rao, Z., Cheng, G.

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Funding Organization	Location	Grant Number
Other government	United States	2019-I2M-5-049
Other government	United States	2016-I2M-1-005
Other government	United States	2019XK310002
National Natural Science Foundation of China (NSFC)	United States	91542201, 81925025, 82102371 and 81802870
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	R01AI069120, AI158154 and AI140718

Revision History  

• Version 1.0: 2021-11-03
  Type: Initial release
  
• Version 1.1: 2022-11-16
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description