7Y0W

Local structure of BD55-5514 and BD55-5840 Fab and Omicron BA.1 RBD complex


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 1.1 of the entry. See complete history


Literature

Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents.

Cao, Y.Jian, F.Zhang, Z.Yisimayi, A.Hao, X.Bao, L.Yuan, F.Yu, Y.Du, S.Wang, J.Xiao, T.Song, W.Zhang, Y.Liu, P.An, R.Wang, P.Wang, Y.Yang, S.Niu, X.Zhang, Y.Gu, Q.Shao, F.Hu, Y.Yin, W.Zheng, A.Wang, Y.Qin, C.Jin, R.Xiao, J.Xie, X.S.

(2022) Cell Rep 41: 111845-111845

  • DOI: https://doi.org/10.1016/j.celrep.2022.111845
  • Primary Citation of Related Structures:  
    7WRY, 7Y0C, 7Y0V, 7Y0W

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages have escaped most receptor-binding domain (RBD)-targeting therapeutic neutralizing antibodies (NAbs), which proves that previous NAb drug screening strategies are deficient against the fast-evolving SARS-CoV-2. Better broad NAb drug candidate selection methods are needed. Here, we describe a rational approach for identifying RBD-targeting broad SARS-CoV-2 NAb cocktails. Based on high-throughput epitope determination, we propose that broad NAb drugs should target non-immunodominant RBD epitopes to avoid herd-immunity-directed escape mutations. Also, their interacting antigen residues should focus on sarbecovirus conserved sites and associate with critical viral functions, making the antibody-escaping mutations less likely to appear. Following these criteria, a featured non-competing antibody cocktail, SA55+SA58, is identified from a large collection of broad sarbecovirus NAbs isolated from SARS-CoV-2-vaccinated SARS convalescents. SA55+SA58 potently neutralizes ACE2-utilizing sarbecoviruses, including circulating Omicron variants, and could serve as broad SARS-CoV-2 prophylactics to offer long-term protection, especially for individuals who are immunocompromised or with high-risk comorbidities.


  • Organizational Affiliation

    Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China; Changping Laboratory, Beijing, P.R. China. Electronic address: yunlongcao@pku.edu.cn.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BD55-5514H123Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BD55-5514L107Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
BD55-5840HC [auth H]119Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
BD55-5840LD [auth L]109Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1E [auth R]193Homo sapiensMutation(s): 16 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
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Go to UniProtKB:  P0DTC2
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UniProt GroupP0DTC2
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  • Reference Sequence
Oligosaccharides

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Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF [auth X]3N/A
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references