9J5U | pdb_00009j5u

Cryo-EM structure of Bat SARS-like coronavirus Khosta-2 spike protein

PDB DOI: https://doi.org/10.2210/pdb9J5U/pdb
EM Map EMD-61152: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Bat SARS-like coronavirus Khosta-2
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-08-13 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: 2.25 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: 429.15 kDa
Atom Count: 27,152
Modeled Residue Count: 3,309
Deposited Residue Count: 3,687
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	1,229	Bat SARS-like coronavirus Khosta-2	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 16	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, G, J	3		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain G Focus chain J Interactions & Density Focus chain D Focus chain F Focus chain G Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
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	AA [auth a], E, H, N, S, AA [auth a], E, H, N, S, Y	4		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain E Focus chain H Focus chain N Focus chain S Focus chain Y Interactions & Density Focus chain AA [auth a] Focus chain E Focus chain H Focus chain N Focus chain S Focus chain Y
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	4		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	BA [auth b], K, M, O, P, BA [auth b], K, M, O, P, Q, R, U, V, W, X, Z	2		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain K Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Z Interactions & Density Focus chain BA [auth b] Focus chain K Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain U Focus chain V Focus chain W Focus chain X Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, T	2		N-Glycosylation	Interactions Focus chain L Focus chain T Interactions & Density Focus chain L Focus chain T
Glycosylation Resources
GlyTouCan: G90333CG GlyCosmos: G90333CG GlyGen: G90333CG

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLA (Subject of Investigation/LOI) Query on BLA Download Ideal Coordinates CCD File SDF format, chain TA [auth B] SDF format, chain IA [auth A] SDF format, chain AB [auth C] MOL2 format, chain TA [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain AB [auth C] mmCIF format, chain TA [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain AB [auth C]	AB [auth C], IA [auth A], TA [auth B]	BILIVERDINE IX ALPHA C₃₃ H₃₄ N₄ O₆ GWZYPXHJIZCRAJ-SRVCBVSDSA-N		Interactions Focus chain AB [auth C] Focus chain IA [auth A] Focus chain TA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain IA [auth A] Focus chain TA [auth B]
EIC (Subject of Investigation/LOI) Query on EIC Download Ideal Coordinates CCD File SDF format, chain SA [auth B] SDF format, chain LA [auth B] SDF format, chain KA [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth A]	KA [auth A], LA [auth B], SA [auth B]	LINOLEIC ACID C₁₈ H₃₂ O₂ OYHQOLUKZRVURQ-HZJYTTRNSA-N		Interactions Focus chain KA [auth A] Focus chain LA [auth B] Focus chain SA [auth B] Interactions & Density Focus chain KA [auth A] Focus chain LA [auth B] Focus chain SA [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain UA [auth C] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain NA [auth B] SDF format, chain MA [auth B] SDF format, chain JA [auth A] SDF format, chain HA [auth A] SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain BB [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain BB [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain BB [auth C]	BB [auth C] CA [auth A] DA [auth A] EA [auth A] FA [auth A] BB [auth C], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], JA [auth A], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], UA [auth C], VA [auth C], 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 CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain JA [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain UA [auth C] Focus chain VA [auth C] 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 CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain JA [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]