9AU1

SARS-CoV-2 XBB.1.5 RBD bound to the VIR-7229 and the S309 Fab fragments


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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 

  • 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
S309 Fab heavy chainA [auth M]230Homo 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
S309 Fab light chainB [auth N]212Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VIR-7229 Fab heavy chainC [auth H]225Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VIR-7229 Fab light chainD [auth L]216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
SARS-CoV-2 XBB.1.5 RBDE [auth R]250Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Entity Groups  
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Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
I [auth L]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
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
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth H],
J [auth R]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
H [auth L]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth N]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
D [auth L]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.726α = 90
b = 112.525β = 90
c = 170.314γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report



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