8TC0

Cryo-EM Structure of Spike Glycoprotein from Bat Coronavirus WIV1 in Closed Conformation

PDB DOI: https://doi.org/10.2210/pdb8TC0/pdb
EM Map EMD-41149: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Rhinolophus sinicus
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2023-06-29 Released: 2024-05-01
Deposition Author(s): Bostina, M., Hills, F.R., Eruera, A.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 1.88 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

Cryo-EM reveals variation in structural motifs within animal SARS-related coronavirus spike proteins

Bostina, M., Hills, F.R., Eruera, A.

To be published.

Macromolecule Content

Total Structure Weight: 392.68 kDa
Atom Count: 26,931
Modelled Residue Count: 3,273
Deposited Residue Count: 3,327
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,109	Rhinolophus sinicus	Mutation(s): 0
UniProt
Find proteins for U5WI05 (Bat SARS-like coronavirus WIV1) Explore U5WI05 Go to UniProtKB: U5WI05
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U5WI05
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, DA [auth d], EA [auth e], H, HA [auth h], D, DA [auth d], EA [auth e], H, HA [auth h], I, L, O, S, T, W, Z	3		N-Glycosylation	Interactions Focus chain D Focus chain DA [auth d] Focus chain EA [auth e] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain L Focus chain O Focus chain S Focus chain T Focus chain W Focus chain Z Interactions & Density Focus chain D Focus chain DA [auth d] Focus chain EA [auth e] Focus chain H Focus chain HA [auth h] Focus chain I Focus chain L Focus chain O Focus chain S Focus chain T Focus chain W Focus chain Z
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

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	AA [auth a], E, P	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain E Focus chain P Interactions & Density Focus chain AA [auth a] Focus chain E Focus chain P
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
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	BA [auth b], CA [auth c], F, FA [auth f], G, BA [auth b], CA [auth c], F, FA [auth f], G, J, Q, R, U	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain CA [auth c] Focus chain F Focus chain FA [auth f] Focus chain G Focus chain J Focus chain Q Focus chain R Focus chain U Interactions & Density Focus chain BA [auth b] Focus chain CA [auth c] Focus chain F Focus chain FA [auth f] Focus chain G Focus chain J Focus chain Q Focus chain R Focus chain U
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	GA [auth g], IA [auth i], JA [auth j], K, M, GA [auth g], IA [auth i], JA [auth j], K, M, N, V, X, Y	4		N-Glycosylation	Interactions Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K Focus chain M Focus chain N Focus chain V Focus chain X Focus chain Y Interactions & Density Focus chain GA [auth g] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain K Focus chain M Focus chain N Focus chain V Focus chain X Focus chain Y
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EIC Query on EIC Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain OA [auth A] SDF format, chain UA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain UA [auth B]	AB [auth C], OA [auth A], UA [auth B]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain AB [auth C] Focus chain OA [auth A] Focus chain UA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain OA [auth A] Focus chain UA [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain PA [auth A] 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 VA [auth B] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain PA [auth A] 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 VA [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C]	BB [auth C] KA [auth A] LA [auth A] MA [auth A] NA [auth A] BB [auth C], KA [auth A], LA [auth A], MA [auth A], NA [auth A], PA [auth A], QA [auth B], RA [auth B], SA [auth B], TA [auth B], VA [auth B], WA [auth C], 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 BB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain PA [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain BB [auth C] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain PA [auth A] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain VA [auth B] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]