8GTO | pdb_00008gto

cryo-EM structure of Omicron BA.5 S protein in complex with XGv282

PDB DOI: https://doi.org/10.2210/pdb8GTO/pdb
EM Map EMD-34259: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-09-08 Released: 2023-07-12
Deposition Author(s): Xia, X.Y., Zhang, Y.Y., Chi, X.M., Huang, B.D., Wu, L.S., Zhou, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 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

Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against SARS-CoV-2 Omicron variants.

Chi, X., Xia, L., Zhang, G., Chi, X., Huang, B., Zhang, Y., Chen, Z., Han, J., Wu, L., Li, Z., Sun, H., Huang, P., Yu, C., Chen, W., Zhou, Q.

(2023) Cell Discov 9: 37-37

PubMed: 37015915 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-023-00535-1
Primary Citation Related Structures:
8GTO, 8GTP, 8GTQ

PubMed Abstract:
The pandemic of COVID-19 caused by SARS-CoV-2 continues to spread around the world. Mutant strains of SARS-CoV-2 are constantly emerging. At present, Omicron variants have become mainstream. In this work, we carried out a systematic and comprehensive analysis of the reported spike protein antibodies, counting the epitopes and genotypes of these antibodies. We further comprehensively analyzed the impact of Omicron mutations on antibody epitopes and classified these antibodies according to their binding patterns. We found that the epitopes of the H-RBD class antibodies were significantly less affected by Omicron mutations than other classes. Binding and virus neutralization experiments showed that such antibodies could effectively inhibit the immune escape of Omicron. Cryo-EM results showed that this class of antibodies utilized a conserved mechanism to neutralize SARS-CoV-2. Our results greatly help us deeply understand the impact of Omicron mutations. Meanwhile, it also provides guidance and insights for developing Omicron antibodies and vaccines.

Organizational Affiliation

Institute of Biotechnology, Academy of Military Medical Sciences, Beijing, China.

Macromolecule Content

Total Structure Weight: 512.25 kDa
Atom Count: 30,234
Modeled Residue Count: 3,759
Deposited Residue Count: 4,497
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,271	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 34 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain of XGv282	D [auth H], F [auth I], H [auth J]	117	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain of XGv282	E [auth L], G [auth M], I [auth N]	111	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], J [auth D], K [auth E], L [auth F], M [auth G], AA [auth a], J [auth D], K [auth E], L [auth F], M [auth G], N [auth K], O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Focus chain M [auth G] Focus chain N [auth K] Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Focus chain M [auth G] Focus chain N [auth K] Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BA [auth A] SDF format, chain BB [auth C] SDF format, chain CA [auth A] SDF format, chain CB [auth C] SDF format, chain DA [auth A] SDF format, chain DB [auth C] SDF format, chain EA [auth A] SDF format, chain EB [auth C] SDF format, chain FA [auth A] SDF format, chain FB [auth C] SDF format, chain GA [auth A] SDF format, chain GB [auth C] SDF format, chain HA [auth A] SDF format, chain HB [auth C] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain UA [auth B] SDF format, chain VA [auth B] SDF format, chain WA [auth B] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth C] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	AB [auth C] BA [auth A] BB [auth C] CA [auth A] CB [auth C] AB [auth C], BA [auth A], BB [auth C], CA [auth A], CB [auth C], DA [auth A], DB [auth C], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth C], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BA [auth A] Focus chain BB [auth C] Focus chain CA [auth A] Focus chain CB [auth C] Focus chain DA [auth A] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]