7LJR

SARS-CoV-2 Spike Protein Trimer bound to DH1043 fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 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

The functions of SARS-CoV-2 neutralizing and infection-enhancing antibodies in vitro and in mice and nonhuman primates.

Li, D.Edwards, R.J.Manne, K.Martinez, D.R.Schafer, A.Alam, S.M.Wiehe, K.Lu, X.Parks, R.Sutherland, L.L.Oguin, T.H.McDanal, C.Perez, L.G.Mansouri, K.Gobeil, S.M.C.Janowska, K.Stalls, V.Kopp, M.Cai, F.Lee, E.Foulger, A.Hernandez, G.E.Sanzone, A.Tilahun, K.Jiang, C.Tse, L.V.Bock, K.W.Minai, M.Nagata, B.M.Cronin, K.Gee-Lai, V.Deyton, M.Barr, M.Von Holle, T.Macintyre, A.N.Stover, E.Feldman, J.Hauser, B.M.Caradonna, T.M.Scobey, T.D.Moody, M.A.Cain, D.W.DeMarco, C.T.Denny, T.N.Woods, C.W.Petzold, E.W.Schmidt, A.G.Teng, I.T.Zhou, T.Kwong, P.D.Mascola, J.R.Graham, B.S.Moore, I.N.Seder, R.Andersen, H.Lewis, M.G.Montefiori, D.C.Sempowski, G.D.Baric, R.S.Acharya, P.Haynes, B.F.Saunders, K.O.

(2021) Biorxiv 

  • DOI: https://doi.org/10.1101/2020.12.31.424729
  • Primary Citation of Related Structures:  
    7LJR

  • PubMed Abstract: 

    SARS-CoV-2 neutralizing antibodies (NAbs) protect against COVID-19. A concern regarding SARS-CoV-2 antibodies is whether they mediate disease enhancement. Here, we isolated NAbs against the receptor-binding domain (RBD) and the N-terminal domain (NTD) of SARS-CoV-2 spike from individuals with acute or convalescent SARS-CoV-2 or a history of SARS-CoV-1 infection. Cryo-electron microscopy of RBD and NTD antibodies demonstrated function-specific modes of binding. Select RBD NAbs also demonstrated Fc receptor-γ (FcγR)-mediated enhancement of virus infection in vitro , while five non-neutralizing NTD antibodies mediated FcγR-independent in vitro infection enhancement. However, both types of infection-enhancing antibodies protected from SARS-CoV-2 replication in monkeys and mice. Nonetheless, three of 31 monkeys infused with enhancing antibodies had higher lung inflammation scores compared to controls. One monkey had alveolar edema and elevated bronchoalveolar lavage inflammatory cytokines. Thus, while in vitro antibody-enhanced infection does not necessarily herald enhanced infection in vivo , increased lung inflammation can occur in SARS-CoV-2 antibody-infused macaques.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab DH1043 heavy chainD [auth S]472Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab DH1043 light chainE [auth T]233Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI145687

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references