7RAL | pdb_00007ral

SARS-CoV-2 S bound to S2X259 Fab (local refinement of the RBD/S2X259 variable domains)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7RAL

This is version 1.3 of the entry. See complete history

Literature

Broad sarbecovirus neutralization by a human monoclonal antibody.

Tortorici, M.A.Czudnochowski, N.Starr, T.N.Marzi, R.Walls, A.C.Zatta, F.Bowen, J.E.Jaconi, S.Di Iulio, J.Wang, Z.De Marco, A.Zepeda, S.K.Pinto, D.Liu, Z.Beltramello, M.Bartha, I.Housley, M.P.Lempp, F.A.Rosen, L.E.Dellota Jr., E.Kaiser, H.Montiel-Ruiz, M.Zhou, J.Addetia, A.Guarino, B.Culap, K.Sprugasci, N.Saliba, C.Vetti, E.Giacchetto-Sasselli, I.Fregni, C.S.Abdelnabi, R.Foo, S.C.Havenar-Daughton, C.Schmid, M.A.Benigni, F.Cameroni, E.Neyts, J.Telenti, A.Virgin, H.W.Whelan, S.P.J.Snell, G.Bloom, J.D.Corti, D.Veesler, D.Pizzuto, M.S.

(2021) Nature 597: 103-108

  • DOI: https://doi.org/10.1038/s41586-021-03817-4
  • Primary Citation Related Structures: 
    7RA8, 7RAL

  • PubMed Abstract: 

    The recent emergence of SARS-CoV-2 variants of concern 1-10 and the recurrent spillovers of coronaviruses 11,12 into the human population highlight the need for broadly neutralizing antibodies that are not affected by the ongoing antigenic drift and that can prevent or treat future zoonotic infections. Here we describe a human monoclonal antibody designated S2X259, which recognizes a highly conserved cryptic epitope of the receptor-binding domain and cross-reacts with spikes from all clades of sarbecovirus. S2X259 broadly neutralizes spike-mediated cell entry of SARS-CoV-2, including variants of concern (B.1.1.7, B.1.351, P.1, and B.1.427/B.1.429), as well as a wide spectrum of human and potentially zoonotic sarbecoviruses through inhibition of angiotensin-converting enzyme 2 (ACE2) binding to the receptor-binding domain. Furthermore, deep-mutational scanning and in vitro escape selection experiments demonstrate that S2X259 possesses an escape profile that is limited to a single substitution, G504D. We show that prophylactic and therapeutic administration of S2X259 protects Syrian hamsters (Mesocricetus auratus) against challenge with the prototypic SARS-CoV-2 and the B.1.351 variant of concern, which suggests that this monoclonal antibody is a promising candidate for the prevention and treatment of emergent variants and zoonotic infections. Our data reveal a key antigenic site that is targeted by broadly neutralizing antibodies and will guide the design of vaccines that are effective against all sarbecoviruses.


  • Organizational Affiliation
    • Department of Biochemistry, University of Washington, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 168.11 kDa 
  • Atom Count: 2,847 
  • Modeled Residue Count: 389 
  • Deposited Residue Count: 1,527 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S2X259 Fab heavy chainA [auth H]126Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
S2X259 Fab light chainB [auth L]113Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoproteinC [auth B]1,288Severe acute respiratory syndrome coronavirus 2Mutation(s): 9 
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
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
D [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 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 Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-09-15
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-03-19
    Changes: Data collection, Data processing