8PQ2

XBB 1.0 RBD bound to P4J15 (Local)

• PDB DOI: https://doi.org/10.2210/pdb8PQ2/pdb
• EM Map EMD-17819: EMDB EMDataResource

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


• Deposited: 2023-07-10 Released: 2023-11-01 
• Deposition Author(s): Duhoo, Y., Lau, K.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Broadly potent anti-SARS-CoV-2 antibody shares 93% of epitope with ACE2 and provides full protection in monkeys.

Fenwick, C., Turelli, P., Duhoo, Y., Lau, K., Herate, C., Marlin, R., Lamrayah, M., Campos, J., Esteves-Leuenberger, L., Farina, A., Raclot, C., Genet, V., Fiscalini, F., Cesborn, J., Perez, L., Dereuddre-Bosquet, N., Contreras, V., Lheureux, K., Relouzat, F., Abdelnabi, R., Leyssen, P., Levy, Y., Pojer, F., Le Grand, R., Trono, D., Pantaleo, G.

(2023) J Infect 87: 524-537

• PubMed: 37852477 
• DOI: https://doi.org/10.1016/j.jinf.2023.10.008
• Primary Citation of Related Structures:  
  8PQ2, 8PSD


• PubMed Abstract: 
  

  Due to the rapid evolution of SARS-CoV-2 to variants with reduced sensitivity to vaccine-induced humoral immunity and the near complete loss of protective efficacy of licensed therapeutic monoclonal antibodies, we isolated a potent, broad-spectrum neutralizing antibody that could potentially provide prophylactic protection to immunocompromised patient populations.

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Organizational Affiliation: 

Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 47.26 kDa 
• Atom Count: 3,065 
• Modelled Residue Count: 390 
• Deposited Residue Count: 423 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P4J15 Fragment Antigen-Binding Heavy Chain	A [auth H]	121	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P4J15 Fragment Antigen-Binding Light Chain	B [auth L]	107	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S2'	C	195	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-01 
Deposition Author(s): Duhoo, Y., Lau, K.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History  

• Version 1.0: 2023-11-01
  Type: Initial release
  
• Version 1.1: 2023-12-06
  Changes: Database references