7WHZ

SARS-CoV-2 spike protein in complex with three human neutralizing antibodies


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Three SARS-CoV-2 antibodies provide broad and synergistic neutralization against variants of concern, including Omicron.

Wang, S.Sun, H.Zhang, Y.Yuan, L.Wang, Y.Zhang, T.Wang, S.Zhang, J.Yu, H.Xiong, H.Tang, Z.Liu, L.Huang, Y.Chen, X.Li, T.Ying, D.Liu, C.Chen, Z.Yuan, Q.Zhang, J.Cheng, T.Li, S.Guan, Y.Zheng, Q.Zheng, Z.Xia, N.

(2022) Cell Rep 39: 110862-110862

  • DOI: 10.1016/j.celrep.2022.110862
  • Primary Citation of Related Structures:  
    7WHZ, 7WI0

  • PubMed Abstract: 
  • The rapidly spreading Omicron variant is highly resistant to vaccines, convalescent sera, and neutralizing antibodies (nAbs), highlighting the urgent need for potent therapeutic nAbs. Here, a panel of human nAbs from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent patients show diverse neutralization against Omicron, of which XMA01 and XMA04 maintain nanomolar affinities and excellent neutralization (half maximal inhibitory concentration [IC50]: ∼20 ng/mL) ...

    The rapidly spreading Omicron variant is highly resistant to vaccines, convalescent sera, and neutralizing antibodies (nAbs), highlighting the urgent need for potent therapeutic nAbs. Here, a panel of human nAbs from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent patients show diverse neutralization against Omicron, of which XMA01 and XMA04 maintain nanomolar affinities and excellent neutralization (half maximal inhibitory concentration [IC50]: ∼20 ng/mL). nAb XMA09 shows weak but unattenuated neutralization against all variants of concern (VOCs) as well as SARS-CoV. Structural analysis reveals that the above three antibodies could synergistically bind to the receptor-binding domains (RBDs) of both wild-type and Omicron spikes and defines the critical determinants for nAb-mediated broad neutralizations. Three nAbs confer synergistic neutralization against Omicron, resulting from the inter-antibody interaction between XMA04 and XMA01(or XMA09). Furthermore, the XMA01/XMA04 cocktail provides synergistic protection against Beta and Omicron variant infections in hamsters. In summary, our results provide insights for the rational design of antibody cocktail therapeutics or universal vaccines against Omicron.


    Organizational Affiliation

    State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen 361102, China; National Institute of Diagnostics and Vaccine Development in Infectious Diseases, School of Public Health, School of Life Sciences, Xiamen University, Xiamen 361102, China; Research Unit of Frontier Technology of Structural Vaccinology, Chinese Academy of Medical Sciences, Xiamen 361102, China. Electronic address: nsxia@xmu.edu.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1A195Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
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UniProt GroupP0DTC2
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
XMA04 heavy chain variable domainB124Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
XMA01 heavy chain variable domainC122Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
IGL c4029_light_IGKV1-39_IGKJ2D107Homo sapiensMutation(s): 0 
UniProt
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UniProt GroupA0A5C2G4I7
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
IG c934_light_IGKV1-5_IGKJ1E107Homo sapiensMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
XMA09 heavy chain variable domainF [auth H]123Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
IG c1437_light_IGLV1-40_IGLJ1G [auth L]110Homo sapiensMutation(s): 0 
UniProt
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UniProt GroupA0A5C2GVU3
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-22
    Type: Initial release