8PSD

SARS-CoV-2 XBB 1.0 closed conformation.

PDB DOI: https://doi.org/10.2210/pdb8PSD/pdb
EM Map EMD-17850: EMDB EMDataResource

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

Deposited: 2023-07-13 Released: 2023-11-01
Deposition Author(s): Duhoo, Y., Lau, K.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 408.59 kDa
Atom Count: 24,569
Modelled Residue Count: 3,076
Deposited Residue Count: 3,612
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A [auth C], B [auth A], C [auth B]	1,204	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain D [auth C] SDF format, chain DA [auth B] SDF format, chain E [auth C] SDF format, chain EA [auth B] SDF format, chain F [auth C] SDF format, chain FA [auth B] SDF format, chain G [auth C] SDF format, chain GA [auth B] SDF format, chain H [auth C] SDF format, chain HA [auth B] SDF format, chain I [auth C] SDF format, chain IA [auth B] SDF format, chain J [auth C] SDF format, chain JA [auth B] SDF format, chain K [auth C] SDF format, chain KA [auth B] SDF format, chain L [auth C] SDF format, chain LA [auth B] SDF format, chain M [auth C] SDF format, chain MA [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth C] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth C] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth C] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth C] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A]	AA [auth A] BA [auth B] CA [auth B] D [auth C] DA [auth B] AA [auth A], BA [auth B], CA [auth B], D [auth C], DA [auth B], E [auth C], EA [auth B], F [auth C], FA [auth B], G [auth C], GA [auth B], H [auth C], HA [auth B], I [auth C], IA [auth B], J [auth C], JA [auth B], K [auth C], KA [auth B], L [auth C], LA [auth B], M [auth C], MA [auth B], N [auth C], O [auth C], P [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth C] Focus chain DA [auth B] Focus chain E [auth C] Focus chain EA [auth B] Focus chain F [auth C] Focus chain FA [auth B] Focus chain G [auth C] Focus chain GA [auth B] Focus chain H [auth C] Focus chain HA [auth B] Focus chain I [auth C] Focus chain IA [auth B] Focus chain J [auth C] Focus chain JA [auth B] Focus chain K [auth C] Focus chain KA [auth B] Focus chain L [auth C] Focus chain LA [auth B] Focus chain M [auth C] Focus chain MA [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth C] Focus chain DA [auth B] Focus chain E [auth C] Focus chain EA [auth B] Focus chain F [auth C] Focus chain FA [auth B] Focus chain G [auth C] Focus chain GA [auth B] Focus chain H [auth C] Focus chain HA [auth B] Focus chain I [auth C] Focus chain IA [auth B] Focus chain J [auth C] Focus chain JA [auth B] Focus chain K [auth C] Focus chain KA [auth B] Focus chain L [auth C] Focus chain LA [auth B] Focus chain M [auth C] Focus chain MA [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]