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 

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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
  • Primary Citation of Related Structures:  
    7BZ5

  • PubMed Abstract: 

    • Neutralizing antibodies could potentially be used as antivirals against the coronavirus disease 2019 (COVID-19) pandemic. Here, we report isolation of four human-origin monoclonal antibodies from a convalescent patient, all of which display neutralization abilities ...

    Neutralizing antibodies could potentially be used as antivirals against the coronavirus disease 2019 (COVID-19) pandemic. Here, we report isolation of four human-origin monoclonal antibodies from a convalescent patient, all of which display neutralization abilities. The antibodies B38 and H4 block binding between the spike glycoprotein receptor binding domain (RBD) of the virus and the cellular receptor angiotensin-converting enzyme 2 (ACE2). A competition assay indicated different epitopes on the RBD for these two antibodies, making them a potentially promising virus-targeting monoclonal antibody pair for avoiding 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1A229Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heavy chain of B38B [auth H]222Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Light chain of B38C [auth L]218Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
D [auth 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

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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  (Full details and data files)

  • 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
  • Version 1.4: 2021-03-10
    Changes: Structure summary