7JVC

SARS-CoV-2 spike in complex with the S2A4 neutralizing antibody Fab fragment


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 1.3 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 found that both the magnitude of Ab responses to SARS-CoV-2 spike (S) and nucleoprotein and nAb titers correlate with clinical scores ...

    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
Spike glycoproteinA, D [auth B], G [auth E]1281Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
Gene Names: S2
UniProt
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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S2A4 Fab heavy chainE [auth C], H [auth F], B [auth H]228Homo 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
S2A4 Fab light chainF [auth D], I [auth G], C [auth L]217Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
J [auth I], K [auth J], M, N, O, P, R, S
J [auth I], K [auth J], M, N, O, P, R, S, T, U, W, X
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseL [auth K], Q, V3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth E] , BA [auth A] , BB [auth E] , CA [auth A] , CB [auth E] , DA [auth A] , DB [auth E] , 
AA [auth A],  AB [auth E],  BA [auth A],  BB [auth E],  CA [auth A],  CB [auth E],  DA [auth A],  DB [auth E],  EA [auth A],  EB [auth E],  FA [auth A],  GA [auth A],  HA [auth A],  IA [auth A],  JA [auth B],  KA [auth B],  LA [auth B],  MA [auth B],  NA [auth B],  OA [auth B],  PA [auth B],  QA [auth B],  RA [auth B],  SA [auth B],  TA [auth B],  UA [auth E],  VA [auth E],  WA [auth E],  XA [auth E],  Y [auth A],  YA [auth E],  Z [auth A],  ZA [auth E]
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: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM120553

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-14
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2021-01-27
    Changes: Structure summary
  • Version 1.3: 2021-06-23
    Changes: Other, Structure summary