7R7N

SARS-CoV-2 spike in complex with the S2D106 neutralizing antibody Fab fragment (local refinement of the RBD and S2D106)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape.

Starr, T.N.Czudnochowski, N.Liu, Z.Zatta, F.Park, Y.J.Addetia, A.Pinto, D.Beltramello, M.Hernandez, P.Greaney, A.J.Marzi, R.Glass, W.G.Zhang, I.Dingens, A.S.Bowen, J.E.Tortorici, M.A.Walls, A.C.Wojcechowskyj, J.A.De Marco, A.Rosen, L.E.Zhou, J.Montiel-Ruiz, M.Kaiser, H.Dillen, J.R.Tucker, H.Bassi, J.Silacci-Fregni, C.Housley, M.P.di Iulio, J.Lombardo, G.Agostini, M.Sprugasci, N.Culap, K.Jaconi, S.Meury, M.Dellota Jr., E.Abdelnabi, R.Foo, S.C.Cameroni, E.Stumpf, S.Croll, T.I.Nix, J.C.Havenar-Daughton, C.Piccoli, L.Benigni, F.Neyts, J.Telenti, A.Lempp, F.A.Pizzuto, M.S.Chodera, J.D.Hebner, C.M.Virgin, H.W.Whelan, S.P.J.Veesler, D.Corti, D.Bloom, J.D.Snell, G.

(2021) Nature 597: 97-102

  • DOI: https://doi.org/10.1038/s41586-021-03807-6
  • Primary Citation of Related Structures:  
    7M7W, 7R6W, 7R6X, 7R7N

  • PubMed Abstract: 

    An ideal therapeutic anti-SARS-CoV-2 antibody would resist viral escape 1-3 , have activity against diverse sarbecoviruses 4-7 , and be highly protective through viral neutralization 8-11 and effector functions 12,13 . Understanding how these properties relate to each other and vary across epitopes would aid the development of therapeutic antibodies and guide vaccine design. Here we comprehensively characterize escape, breadth and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD). Despite a trade-off between in vitro neutralization potency and breadth of sarbecovirus binding, we identify neutralizing antibodies with exceptional sarbecovirus breadth and a corresponding resistance to SARS-CoV-2 escape. One of these antibodies, S2H97, binds with high affinity across all sarbecovirus clades to a cryptic epitope and prophylactically protects hamsters from viral challenge. Antibodies that target the angiotensin-converting enzyme 2 (ACE2) receptor-binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency. Nevertheless, we also characterize a potent RBM antibody (S2E12 8 ) with breadth across sarbecoviruses related to SARS-CoV-2 and a high barrier to viral escape. These data highlight principles underlying variation in escape, breadth and potency among antibodies that target the RBD, and identify epitopes and features to prioritize for therapeutic development against the current and potential future pandemics.


  • Organizational Affiliation

    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S2D106 FAB heavy chainA [auth H]126Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinB [auth E]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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
S2D106 FAB light chainC [auth L]107Homo sapiensMutation(s): 0 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth A]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.95 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: 2021-07-21
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2021-09-15
    Changes: Database references