7EK0

Complex Structure of antibody BD-503 and RBD-N501Y of COVID-19

• PDB DOI: https://doi.org/10.2210/pdb7EK0/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2021-04-03 Released: 2022-04-13 
• Deposition Author(s): Xu, H., Wang, B., Zhao, T.N., Su, X.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.214 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Structure-based analyses of neutralization antibodies interacting with naturally occurring SARS-CoV-2 RBD variants.

Xu, H., Wang, B., Zhao, T.N., Liang, Z.T., Peng, T.B., Song, X.H., Wu, J.J., Wang, Y.C., Su, X.D.

(2021) Cell Res 31: 1126-1129

• PubMed: 34480123 
• DOI: https://doi.org/10.1038/s41422-021-00554-1
• Primary Citation of Related Structures:  
  7EJY, 7EJZ, 7EK0, 7F6Y, 7F6Z

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Organizational Affiliation: 

State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 71.8 kDa 
• Atom Count: 4,747 
• Modelled Residue Count: 621 
• Deposited Residue Count: 660 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A [auth R]	223	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of BD-503	B [auth H]	222	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of BD-503	C [auth L]	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.266 
• R-Value Work: 0.214 
• R-Value Observed: 0.218 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.426	α = 90
b = 149.665	β = 90
c = 146.433	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-04-13 
Deposition Author(s): Xu, H., Wang, B., Zhao, T.N., Su, X.D.

Revision History  

• Version 1.0: 2022-04-13
  Type: Initial release
  
• Version 1.1: 2022-11-02
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary