7T9J | pdb_00007t9j

Cryo-EM structure of the SARS-CoV-2 Omicron spike protein

PDB DOI: https://doi.org/10.2210/pdb7T9J/pdb
EM Map EMD-25759: EMDB EMDataResource

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

Deposited: 2021-12-19 Released: 2021-12-29
Deposition Author(s): Zhu, X., Mannar, D., Saville, J.W., Srivastava, S.S., Berezuk, A.M., Tuttle, K.S., Subramaniam, S.
Funding Organization(s): Canada Excellence Research Chair Award, Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex.

Mannar, D., Saville, J.W., Zhu, X., Srivastava, S.S., Berezuk, A.M., Tuttle, K.S., Marquez, A.C., Sekirov, I., Subramaniam, S.

(2022) Science 375: 760-764

PubMed: 35050643 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.abn7760
Primary Citation Related Structures:
7T9J, 7T9K, 7T9L

PubMed Abstract:
The newly reported Omicron variant is poised to replace Delta as the most prevalent SARS-CoV-2 variant across the world. Cryo-EM structural analysis of the Omicron variant spike protein in complex with human ACE2 reveals new salt bridges and hydrogen bonds formed by mutated residues R493, S496 and R498 in the RBD with ACE2. These interactions appear to compensate for other Omicron mutations such as K417N known to reduce ACE2 binding affinity, resulting in similar biochemical ACE2 binding affinities for Delta and Omicron variants. Neutralization assays show that pseudoviruses displaying the Omicron spike protein exhibit increased antibody evasion. The increase in antibody evasion, together with retention of strong interactions at the ACE2 interface, thus represent important molecular features that likely contribute to the rapid spread of the Omicron variant.

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.

Macromolecule Content

Total Structure Weight: 440.26 kDa
Atom Count: 21,960
Modeled Residue Count: 2,703
Deposited Residue Count: 3,855
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,285	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 10 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: 13	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G, H D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Interactions & Density Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 A] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain KA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain W [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain V [auth A] SDF format, chain QA [auth C] SDF format, chain MA [auth C] SDF format, chain LA [auth C] SDF format, chain JA [auth C] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain V [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain V [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	AA [auth A] BA [auth A] CA [auth B] DA [auth B] EA [auth B] AA [auth A], BA [auth A], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth C], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], 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 A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] 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 A] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] 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]