7BZ5

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


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 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


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 368: 1274-1278

  • 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 betw ...

    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.


    Organizational Affiliation

    Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. wuy@biols.ac.cn gaofeng@tib.cas.cn gaof@im.ac.cn liulei3322@aliyun.com.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike protein S1A229Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Heavy chain of B38H222Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Light chain of B38L218Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
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 = 195.226α = 90
b = 86.417β = 100.19
c = 56.827γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



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.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31872745, 81902058

Revision History 

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary