9J6G | pdb_00009j6g

Cryo-EM structure of Bat SARS-like coronavirus Khosta-1 spike protein

PDB DOI: https://doi.org/10.2210/pdb9J6G/pdb
EM Map EMD-61170: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Bat SARS-like coronavirus Khosta-1
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-08-15 Released: 2025-08-20
Deposition Author(s): Pan, X.Q., Li, L.J., Liu, K.F., Qi, J.X., Gao, G.F.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 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 recognition by Khosta-1/Khosta-2 spike proteins

Pan, X.Q., Li, L.J., Liu, K.F.

To be published.

Macromolecule Content

Total Structure Weight: 401.45 kDa
Atom Count: 26,136
Modeled Residue Count: 3,231
Deposited Residue Count: 3,501
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 [auth B], B [auth A], C	1,167	Bat SARS-like coronavirus Khosta-1	Mutation(s): 0 Gene Names: S
UniProt
Find proteins for A0A8E6M825 (Bat SARS-like coronavirus Khosta-1) Explore A0A8E6M825 Go to UniProtKB: A0A8E6M825
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8E6M825
Glycosylation
Glycosylation Sites: 17	Glycosylation Focus chain A [auth B] Focus chain B [auth A] Focus chain C
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, P	4		N-Glycosylation	Interactions Focus chain D Focus chain P Interactions & Density Focus chain D Focus chain P
Glycosylation Resources
GlyTouCan: G53755TJ GlyCosmos: G53755TJ GlyGen: G53755TJ

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, H, I E, F, G, H, I, J, L, M, N, O, Q, R, S, T	2		N-Glycosylation	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	K	4		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 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 B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] 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 NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain U [auth B] SDF format, chain UA [auth C] SDF format, chain V [auth B] SDF format, chain VA [auth C] SDF format, chain W [auth B] SDF format, chain WA [auth C] SDF format, chain X [auth B] SDF format, chain XA [auth C] SDF format, chain Y [auth B] SDF format, chain YA [auth C] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] 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 NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] 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 NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth C]	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 A], GA [auth A], HA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth A], PA [auth A], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	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 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 NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] 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 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 NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain WA [auth C] Focus chain X [auth B] Focus chain XA [auth C] Focus chain Y [auth B] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]