8XN5

Cryo-EM structure of SARS-CoV-2 Omicron EG.5.1 spike protein(6P) in complex with human ACE2

PDB DOI: https://doi.org/10.2210/pdb8XN5/pdb
EM Map EMD-38498: EMDB EMDataResource

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

Deposited: 2023-12-29 Released: 2024-07-03
Deposition Author(s): Li, L.J., Gu, Y.H., Shi, K.Y., Qi, J.X., Gao, G.F.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of receptor binding and immune escape for SARS-CoV-2 Omicron BA.2.86, EG.5, EG.5.1 and HV.1 sub-variants

Li, L.J., Xu, Z.P., Liu, K.F., Gao, G.F.

To be published.

Macromolecule Content

Total Structure Weight: 487.2 kDa
Atom Count: 29,149
Modelled Residue Count: 3,636
Deposited Residue Count: 4,284
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme 2	A	603	Homo sapiens	Mutation(s): 0 Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1 Go to UniProtKB: Q9BYF1
GTEx: ENSG00000130234
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B, C, D	1,227	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 49 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
Glycosylation
Glycosylation Sites: 11	Glycosylation Focus chain B Focus chain C Focus chain D	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain E [auth A] SDF format, chain EA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain K [auth B] SDF format, chain KA [auth D] SDF format, chain L [auth B] SDF format, chain LA [auth D] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain NA [auth D] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth C] SDF format, chain DA [auth C] SDF format, chain MA [auth D] SDF format, chain OA [auth D] SDF format, chain S [auth B] SDF format, chain X [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth B] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth D] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth C]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] E [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], JA [auth D], K [auth B], KA [auth D], L [auth B], LA [auth D], M [auth B], MA [auth D], N [auth B], NA [auth D], O [auth B], OA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth B] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain E [auth A] Focus chain EA [auth C] Focus chain F [auth A] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain K [auth B] Focus chain KA [auth D] Focus chain L [auth B] Focus chain LA [auth D] Focus chain M [auth B] Focus chain MA [auth D] Focus chain N [auth B] Focus chain NA [auth D] Focus chain O [auth B] Focus chain OA [auth D] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]