7JVA

SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment (local refinement of the receptor-binding domain and Fab variable domains)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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

Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology.

Piccoli, L.Park, Y.J.Tortorici, M.A.Czudnochowski, N.Walls, A.C.Beltramello, M.Silacci-Fregni, C.Pinto, D.Rosen, L.E.Bowen, J.E.Acton, O.J.Jaconi, S.Guarino, B.Minola, A.Zatta, F.Sprugasci, N.Bassi, J.Peter, A.De Marco, A.Nix, J.C.Mele, F.Jovic, S.Rodriguez, B.F.Gupta, S.V.Jin, F.Piumatti, G.Lo Presti, G.Pellanda, A.F.Biggiogero, M.Tarkowski, M.Pizzuto, M.S.Cameroni, E.Havenar-Daughton, C.Smithey, M.Hong, D.Lepori, V.Albanese, E.Ceschi, A.Bernasconi, E.Elzi, L.Ferrari, P.Garzoni, C.Riva, A.Snell, G.Sallusto, F.Fink, K.Virgin, H.W.Lanzavecchia, A.Corti, D.Veesler, D.

(2020) Cell 183: 1024-1042.e21

  • DOI: 10.1016/j.cell.2020.09.037
  • Primary Citation of Related Structures:  
    7JVA, 7JV6, 7JV4, 7JV2, 7JW0, 7JVC, 7JXC, 7JXD, 7JX3, 7JXE

  • PubMed Abstract: 
  • Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we ...

    Analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection is crucial for understanding immune protection and identifying targets for vaccine design. In a cohort of 647 SARS-CoV-2-infected subjects, we found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores. The receptor-binding domain (RBD) is immunodominant and the target of 90% of the neutralizing activity present in SARS-CoV-2 immune sera. Whereas overall RBD-specific serum IgG titers waned with a half-life of 49 days, nAb titers and avidity increased over time for some individuals, consistent with affinity maturation. We structurally defined an RBD antigenic map and serologically quantified serum Abs specific for distinct RBD epitopes leading to the identification of two major receptor-binding motif antigenic sites. Our results explain the immunodominance of the receptor-binding motif and will guide the design of COVID-19 vaccines and therapeutics.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Electronic address: dveesler@uw.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S2A4 Fab heavy chainH119Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S2A4 Fab light chainL111Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SARS-CoV-2 spike glycoproteinA1281Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
3 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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 General Medical Sciences (NIH/NIGMS)United StatesR01GM120553

Revision History 

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references