8ERQ

SARS-CoV-2 BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment (local refinement of the RBD and S2X324)


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

Imprinted antibody responses against SARS-CoV-2 Omicron sublineages.

Park, Y.J.Pinto, D.Walls, A.C.Liu, Z.De Marco, A.Benigni, F.Zatta, F.Silacci-Fregni, C.Bassi, J.Sprouse, K.R.Addetia, A.Bowen, J.E.Stewart, C.Giurdanella, M.Saliba, C.Guarino, B.Schmid, M.A.Franko, N.M.Logue, J.K.Dang, H.V.Hauser, K.di Iulio, J.Rivera, W.Schnell, G.Rajesh, A.Zhou, J.Farhat, N.Kaiser, H.Montiel-Ruiz, M.Noack, J.Lempp, F.A.Janer, J.Abdelnabi, R.Maes, P.Ferrari, P.Ceschi, A.Giannini, O.de Melo, G.D.Kergoat, L.Bourhy, H.Neyts, J.Soriaga, L.Purcell, L.A.Snell, G.Whelan, S.P.J.Lanzavecchia, A.Virgin, H.W.Piccoli, L.Chu, H.Y.Pizzuto, M.S.Corti, D.Veesler, D.

(2022) Science 378: 619-627

  • DOI: https://doi.org/10.1126/science.adc9127
  • Primary Citation of Related Structures:  
    8ERQ, 8ERR

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S2X324 Fab heavy chainA [auth H]119Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S2X324 Fab light chainB [auth L]110Homo 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
Spike glycoproteinC [auth A]1,274Severe acute respiratory syndrome coronavirus 2Mutation(s): 36 
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

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: 2022-10-26
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2022-11-23
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Structure summary