8ZMP | pdb_00008zmp

Cryo-EM structure of the spike glycoprotein from Bat SARS-like coronavirus (Bat SL-CoV) WIV1 in locked state

PDB DOI: https://doi.org/10.2210/pdb8ZMP/pdb
EM Map EMD-60253: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Bat SARS-like coronavirus WIV1
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-05-23 Released: 2025-05-28
Deposition Author(s): Liu, C., Beck, F., Nagy, I., Bohn, S., Plitzko, J., Baumeister, W., Zhang, X., Zinzula, L.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.38 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of the spike glycoprotein from Bat SARS-like coronavirus WIV1

Liu, C., Beck, F., Nagy, I., Bohn, S., Plitzko, J., Baumeister, W., Zhang, X., Zinzula, L.

To be published.

Macromolecule Content

Total Structure Weight: 423.34 kDa
Atom Count: 26,175
Modeled Residue Count: 3,198
Deposited Residue Count: 3,639
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	1,213	Bat SARS-like coronavirus WIV1	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
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A Focus chain B Focus chain C
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)-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], F, H, I, J, K, L, M, O, Q, R, S, T, U, V, X, 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 F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain X 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 F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	E, N, W	3		N-Glycosylation	Interactions Focus chain E Focus chain N Focus chain W Interactions & Density Focus chain E Focus chain N Focus chain W
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, P, Y	4		N-Glycosylation	Interactions Focus chain G Focus chain P Focus chain Y Interactions & Density Focus chain G Focus chain P Focus chain Y
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

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 EA [auth A] SDF format, chain NA [auth B] SDF format, chain WA [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain WA [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain WA [auth C]	EA [auth A], NA [auth B], WA [auth C]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain EA [auth A] Focus chain NA [auth B] Focus chain WA [auth C] Interactions & Density Focus chain EA [auth A] Focus chain NA [auth B] Focus chain WA [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth C] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain OA [auth B] SDF format, chain PA [auth B] 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 UA [auth B] SDF format, chain VA [auth B] SDF format, chain XA [auth C] SDF format, chain YA [auth C] SDF format, chain ZA [auth C] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] 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 UA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain ZA [auth C] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain ZA [auth C]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth C] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth C], FA [auth A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], 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 AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]