9R6T | pdb_00009r6t

Prefusion stabilized spike glycoprotein of equine coronavirus.

PDB DOI: https://doi.org/10.2210/pdb9R6T/pdb
EM Map EMD-53687: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Equine coronavirus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-13 Released: 2026-03-11
Deposition Author(s): Melchers, J.M., Hulswit, R.J.G., Hurdiss, D.L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.76 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

AI-guided prefusion stabilization of the human coronavirus OC43 spike protein enables universal Embecovirus antigen design

Melchers, J.M., Juraszek, J., Hulswit, R.J.G., van Overveld, D., Le, L., van Kuppeveld, F., Hurdiss, D.L., Bosch, B.J., Langedijk, J.P.M., Bakkers, M.J.G.

To be published.

Macromolecule Content

Total Structure Weight: 445.77 kDa
Atom Count: 29,034
Modeled Residue Count: 3,633
Deposited Residue Count: 3,906
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	1,302	Equine coronavirus	Mutation(s): 0
UniProt
Find proteins for R4WAW7 (Equine coronavirus) Explore R4WAW7 Go to UniProtKB: R4WAW7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	R4WAW7
Glycosylation
Glycosylation Sites: 13	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain DA [auth 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 Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain CA [auth c] Focus chain D Focus chain DA [auth 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 Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8Z9 (Subject of Investigation/LOI) Query on 8Z9 Download Ideal Coordinates CCD File SDF format, chain IA [auth A] SDF format, chain NA [auth B] SDF format, chain OA [auth C] MOL2 format, chain IA [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth C] mmCIF format, chain IA [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth C]	IA [auth A], NA [auth B], OA [auth C]	Sapienic acid C₁₆ H₃₀ O₂ NNNVXFKZMRGJPM-KHPPLWFESA-N		Interactions Focus chain IA [auth A] Focus chain NA [auth B] Focus chain OA [auth C] Interactions & Density Focus chain IA [auth A] Focus chain NA [auth B] Focus chain OA [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain MA [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain MA [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain MA [auth B]	EA [auth A] FA [auth A] GA [auth A] HA [auth A] JA [auth B] EA [auth A], FA [auth A], GA [auth A], HA [auth A], JA [auth B], KA [auth B], LA [auth B], MA [auth B], PA [auth C], QA [auth C], RA [auth C], SA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C]