Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1BC 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: 73.36 kDa 
• Atom Count: 5367 
• Residue Count: 628 
• Unique protein chains: 3

7BZ5

Structure of COVID-19 virus spike receptor-binding domain complexed with a neutralizing antibody

• DOI: 10.2210/pdb7BZ5/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Spodoptera frugiperda, Homo sapiens
• Mutation(s): No 


• Deposited: 2020-04-26 Released: 2020-05-13 
• Deposition Author(s): Wu, Y., Qi, J., Gao, F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.191 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2.

Wu, Y., Wang, F., Shen, C., Peng, W., Li, D., Zhao, C., Li, Z., Li, S., Bi, Y., Yang, Y., Gong, Y., Xiao, H., Fan, Z., Tan, S., Wu, G., Tan, W., Lu, X., Fan, C., Wang, Q., Liu, Y., Zhang, C., Qi, J., Gao, G.F., Gao, F., Liu, L.

(2020) Science 

• PubMed: 32404477 
• DOI: 10.1126/science.abc2241
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Neutralizing antibodies could be antivirals against COVID-19 pandemics. Here, we report isolation of four human-origin monoclonal antibodies from a convalescent patient, all of which display neutralization abilities. B38 and H4 block the binding between virus S-protein RBD and cellular receptor ACE2. A competition assay indicates their different epitopes on the RBD, making them a potential virus-targeting MAb-pair to avoid immune escape in future clinical applications. Moreover, a therapeutic study in a mouse model validated that these antibodies can reduce virus titers in infected lungs. The RBD-B38 complex structure revealed that most residues on the epitope overlap with the RBD-ACE2 binding interface, explaining the blocking effect and neutralizing capacity. Our results highlight the promise of antibody-based therapeutics and provide a structural basis for rational vaccine design.

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Organizational Affiliation: 

Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. [e-mail] [e-mail] [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Spike protein S1	A	229	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Heavy chain of B38	H	222	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Light chain of B38	L	218	Homo sapiens	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.191 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.226	α = 90
b = 86.417	β = 100.19
c = 56.827	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-04-26 
• Released Date: 2020-05-13 
Deposition Author(s): Wu, Y., Qi, J., Gao, F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31872745, 81902058

Revision History 

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2020-05-27
  Changes: Database references