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

Validation slider image for 9J5U

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:

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

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	D 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	D 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	D 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	D 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]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History (Full details and data files)

Version 1.0: 2025-08-20
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.