9AU1 | pdb_00009au1

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

• PDB DOI: https://doi.org/10.2210/pdb9AU1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-02-27 Released: 2024-10-16 
• Deposition Author(s): Rietz, T., Park, Y.J., Errico, J., Czudnochowski, N., Nix, J.C., Corti, D., Snell, G., Marco, A.D., Pinto, D., Cameroni, E., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D., Structural Genomics Consortium (SGC)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

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

• PubMed: 39383863 
• DOI: https://doi.org/10.1016/j.cell.2024.09.026
• Primary Citation 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.

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Organizational Affiliation: 
• Vir Biotechnology, San Francisco, CA 94158, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
ProtaBody, Pasadena, CA 91105, USA.
Institut Pasteur, Université Paris Cité, Lyssavirus Epidemiology and Neuropathology Unit, F-75015 Paris, France.
Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA.
Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
Vir Biotechnology, San Francisco, CA 94158, USA; Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
Humabs BioMed SA, a Subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland. Electronic address: [e-mail].
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. Electronic address: [e-mail].
Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 124.04 kDa 
• Atom Count: 8,190 
• Modeled Residue Count: 1,066 
• Deposited Residue Count: 1,133 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 Fab heavy chain	A [auth M]	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S309 Fab light chain	B [auth N]	212	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
VIR-7229 Fab heavy chain	C [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
VIR-7229 Fab light chain	D [auth L]	216	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
SARS-CoV-2 XBB.1.5 RBD	E [auth R]	250	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0
UniProt
Find proteins for A0A8A5XRG7 (Severe acute respiratory syndrome coronavirus 2) Explore A0A8A5XRG7  Go to UniProtKB:  A0A8A5XRG7
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	I [auth L]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG	K [auth R]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	G [auth H], J [auth R]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACY	H [auth L]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
K	F [auth N]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	D [auth L]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.726	α = 90
b = 112.525	β = 90
c = 170.314	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Rietz, T., Park, Y.J., Errico, J., Czudnochowski, N., Nix, J.C., Corti, D., Snell, G., Marco, A.D., Pinto, D., Cameroni, E., Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Database references