8QH1 | pdb_00008qh1

Crystal structure of the SARS-CoV-2 RBD from the Omicron BA4 variant with the antibody Cv2.3194

• PDB DOI: https://doi.org/10.2210/pdb8QH1/pdb

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


• Deposited: 2023-09-06 Released: 2024-06-19 
• Deposition Author(s): Fernandez, I., Rey, F.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Models: experimental, in silico

Literature

Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2.

Planchais, C., Fernandez, I., Chalopin, B., Bruel, T., Rosenbaum, P., Beretta, M., Dimitrov, J.D., Conquet, L., Donati, F., Prot, M., Porrot, F., Planas, D., Staropoli, I., Guivel-Benhassine, F., Baquero, E., van der Werf, S., Haouz, A., Simon-Loriere, E., Montagutelli, X., Maillere, B., Rey, F.A., Guardado-Calvo, P., Nozach, H., Schwartz, O., Mouquet, H.

(2024) iScience 27: 110354-110354

• PubMed: 39071888 
• DOI: https://doi.org/10.1016/j.isci.2024.110354
• Primary Citation Related Structures: 
  8QH0, 8QH1


• PubMed Abstract: 
  

  Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.

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Organizational Affiliation: 
• Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France.
Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France.
CNRS UMR3569, 75015 Paris, France.
CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France.
Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France.
Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006 Paris, France.
Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France.
Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France.
National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France.
Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, 75015 Paris, France.
Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Cristallography Platform-C2RT, 75015 Paris, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.92 kDa 
• Atom Count: 4,753 
• Modeled Residue Count: 619 
• Deposited Residue Count: 683 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth E]	243	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cv2.3194 heavy chain	B [auth H]	229	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IGK@ protein	C [auth L]	211	Homo sapiens	Mutation(s): 0  Gene Names: IGK@
UniProt
Find proteins for Q6PJF2 (Homo sapiens) Explore Q6PJF2  Go to UniProtKB:  Q6PJF2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.793	α = 90
b = 85.348	β = 97.48
c = 193.987	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Fernandez, I., Rey, F.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Structure summary
• Version 1.2: 2025-07-02
  Changes: Database references