7YVL

Omicron BA.4/5 SARS-CoV-2 S RBD in complex with TH272 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.

Guo, Y.Zhang, G.Yang, Q.Xie, X.Lu, Y.Cheng, X.Wang, H.Liang, J.Tang, J.Gao, Y.Shang, H.Dai, J.Shi, Y.Zhou, J.Zhou, J.Guo, H.Yang, H.Qi, J.Liu, L.Ma, S.Zhang, B.Huo, Q.Xie, Y.Wu, J.Dong, F.Zhang, S.Lou, Z.Gao, Y.Song, Z.Wang, W.Sun, Z.Yang, X.Xiong, D.Liu, F.Chen, X.Zhu, P.Wang, X.Cheng, T.Rao, Z.

(2023) Nat Commun 14: 3537-3537

  • DOI: https://doi.org/10.1038/s41467-023-39267-x
  • Primary Citation of Related Structures:  
    7YVE, 7YVF, 7YVG, 7YVH, 7YVI, 7YVJ, 7YVK, 7YVL, 7YVM, 7YVN, 7YVO, 7YVP, 8GOU, 8GPY

  • PubMed Abstract: 

    The SARS-CoV-2 Omicron variant evades most currently approved neutralizing antibodies (nAbs) and caused drastic decrease of plasma neutralizing activity elicited by vaccination or prior infection, urging the need for the development of pan-variant antivirals. Breakthrough infection induces a hybrid immunological response with potentially broad, potent and durable protection against variants, therefore, convalescent plasma from breakthrough infection may provide a broadened repertoire for identifying elite nAbs. We performed single-cell RNA sequencing (scRNA-seq) and BCR sequencing (scBCR-seq) of B cells from BA.1 breakthrough-infected patients who received 2 or 3 previous doses of inactivated vaccine. Elite nAbs, mainly derived from the IGHV2-5 and IGHV3-66/53 germlines, showed potent neutralizing activity across Wuhan-Hu-1, Delta, Omicron sublineages BA.1 and BA.2 at picomolar NT 50 values. Cryo-EM analysis revealed diverse modes of spike recognition and guides the design of cocktail therapy. A single injection of paired antibodies cocktail provided potent protection in the K18-hACE2 transgenic female mouse model of SARS-CoV-2 infection.


  • Organizational Affiliation

    State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 38 Tongyan Road, Tianjin, 300071, China. guoyu@nankai.edu.cn.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TH272 Fab heavy chain119Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TH272 Fab light chainB [auth C]109Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinC [auth B]1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 38 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
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UniProt GroupP0DTC2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870733

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary