7K3Q

An ultra-potent human neutralizing antibody locks the SARS-CoV-2 spike in the closed conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ultrapotent human antibodies protect against SARS-CoV-2 challenge via multiple mechanisms.

Tortorici, M.A.Beltramello, M.Lempp, F.A.Pinto, D.Dang, H.V.Rosen, L.E.McCallum, M.Bowen, J.Minola, A.Jaconi, S.Zatta, F.De Marco, A.Guarino, B.Bianchi, S.Lauron, E.J.Tucker, H.Zhou, J.Peter, A.Havenar-Daughton, C.Wojcechowskyj, J.A.Case, J.B.Chen, R.E.Kaiser, H.Montiel-Ruiz, M.Meury, M.Czudnochowski, N.Spreafico, R.Dillen, J.Ng, C.Sprugasci, N.Culap, K.Benigni, F.Abdelnabi, R.Foo, S.C.Schmid, M.A.Cameroni, E.Riva, A.Gabrieli, A.Galli, M.Pizzuto, M.S.Neyts, J.Diamond, M.S.Virgin, H.W.Snell, G.Corti, D.Fink, K.Veesler, D.

(2020) Science 370: 950-957

  • DOI: https://doi.org/10.1126/science.abe3354
  • Primary Citation of Related Structures:  
    7K3Q, 7K43, 7K45, 7K4N

  • PubMed Abstract: 

    Efficient therapeutic options are needed to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has caused more than 922,000 fatalities as of 13 September 2020. We report the isolation and characterization of two ultrapotent SARS-CoV-2 human neutralizing antibodies (S2E12 and S2M11) that protect hamsters against SARS-CoV-2 challenge. Cryo-electron microscopy structures show that S2E12 and S2M11 competitively block angiotensin-converting enzyme 2 (ACE2) attachment and that S2M11 also locks the spike in a closed conformation by recognition of a quaternary epitope spanning two adjacent receptor-binding domains. Antibody cocktails that include S2M11, S2E12, or the previously identified S309 antibody broadly neutralize a panel of circulating SARS-CoV-2 isolates and activate effector functions. Our results pave the way to implement antibody cocktails for prophylaxis or therapy, circumventing or limiting the emergence of viral escape mutants.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment of S2E12 monoclonal antibody, heavy chainA [auth H]226Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment of S2E12 monoclonal antibody, light chainB [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.38 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.014α = 90
b = 85.722β = 90
c = 86.306γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary