9ELM | pdb_00009elm

Cryo-EM structure of SARS-CoV-2 Omicron JN.1.11 spike protein (closed state)

PDB DOI: https://doi.org/10.2210/pdb9ELM/pdb
EM Map EMD-48155: EMDB EMDataResource

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

Deposited: 2024-12-04 Released: 2025-06-04
Deposition Author(s): Feng, Z., Huang, J., Ward, A.B.
Funding Organization(s): Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.68 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

Structure of SARS-CoV-2 KP.3.1.1 Spike Protein

Feng, Z.

To be published.

Macromolecule Content

Total Structure Weight: 411.88 kDa
Atom Count: 25,275
Modeled Residue Count: 3,117
Deposited Residue Count: 3,600
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,200	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 60
UniProt
Find proteins for A0A6N0C4S6 (Severe acute respiratory syndrome coronavirus 2) Explore A0A6N0C4S6 Go to UniProtKB: A0A6N0C4S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6N0C4S6
Glycosylation
Glycosylation Sites: 12	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, H, I, M, N D, H, I, M, N, R	3		N-Glycosylation	Interactions Focus chain D Focus chain H Focus chain I Focus chain M Focus chain N Focus chain R Interactions & Density Focus chain D Focus chain H Focus chain I Focus chain M Focus chain N Focus chain R

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, J, K E, F, G, J, K, L, O, P, Q	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain J Focus chain K Focus chain L Focus chain O Focus chain P Focus chain Q Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain J Focus chain K Focus chain L Focus chain O Focus chain P Focus chain Q

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 B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] 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 X [auth A] SDF format, chain Y [auth A] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain GA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain W [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] 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 X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth C], MA [auth C], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] 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 B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] 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 B]