9ATM

SARS-CoV-2 EG.5 RBD bound to the VIR-7229 and the S2H97 Fab fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.

Rosen, L.E.Tortorici, M.A.De Marco, A.Pinto, D.Foreman, W.B.Taylor, A.L.Park, Y.J.Bohan, D.Rietz, T.Errico, J.M.Hauser, K.Dang, H.V.Chartron, J.W.Giurdanella, M.Cusumano, G.Saliba, C.Zatta, F.Sprouse, K.R.Addetia, A.Zepeda, S.K.Brown, J.Lee, J.Dellota Jr., E.Rajesh, A.Noack, J.Tao, Q.DaCosta, Y.Tsu, B.Acosta, R.Subramanian, S.de Melo, G.D.Kergoat, L.Zhang, I.Liu, Z.Guarino, B.Schmid, M.A.Schnell, G.Miller, J.L.Lempp, F.A.Czudnochowski, N.Cameroni, E.Whelan, S.P.J.Bourhy, H.Purcell, L.A.Benigni, F.di Iulio, J.Pizzuto, M.S.Lanzavecchia, A.Telenti, A.Snell, G.Corti, D.Veesler, D.Starr, T.N.

(2024) Cell 187: 7196

  • DOI: https://doi.org/10.1016/j.cell.2024.09.026
  • Primary Citation of Related Structures:  
    8S6M, 9ASD, 9ATM, 9AU1, 9AU2

  • PubMed Abstract: 

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has resulted in viral escape from clinically authorized monoclonal antibodies (mAbs), creating a need for mAbs that are resilient to epitope diversification. Broadly neutralizing coronavirus mAbs that are sufficiently potent for clinical development and retain activity despite viral evolution remain elusive. We identified a human mAb, designated VIR-7229, which targets the viral receptor-binding motif (RBM) with unprecedented cross-reactivity to all sarbecovirus clades, including non-ACE2-utilizing bat sarbecoviruses, while potently neutralizing SARS-CoV-2 variants since 2019, including the recent EG.5, BA.2.86, and JN.1. VIR-7229 tolerates extraordinary epitope variability, partly attributed to its high binding affinity, receptor molecular mimicry, and interactions with RBM backbone atoms. Consequently, VIR-7229 features a high barrier for selection of escape mutants, which are rare and associated with reduced viral fitness, underscoring its potential to be resilient to future viral evolution. VIR-7229 is a strong candidate to become a next-generation medicine.


  • Organizational Affiliation

    Vir Biotechnology, San Francisco, CA 94158, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VIR-7229 Fab heavy chainA [auth H]226Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
S2H97 Fab heavy chainB [auth I]223Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VIR-7229 Fab light chainC [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
S2H97 Fab light chainD [auth M]218Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SARS-CoV-2 EG.5 RBDE [auth R]239Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for A0A6V7ALX9 (Severe acute respiratory syndrome coronavirus 2)
Explore A0A6V7ALX9 
Go to UniProtKB:  A0A6V7ALX9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6V7ALX9
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
K [auth R]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
I [auth M]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth I],
J [auth R],
L [auth R]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
G [auth L]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth L]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
B [auth I]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.728α = 90
b = 149.698β = 90
c = 167.078γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00036

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 2.0: 2024-10-23
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-12-25
    Changes: Database references