9KR9 | pdb_00009kr9

Overall structure of HKU5 S protein with S468A/Y463A mutation

PDB DOI: https://doi.org/10.2210/pdb9KR9/pdb
EM Map EMD-62523: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pipistrellus bat coronavirus HKU5
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-11-27 Released: 2025-11-05
Deposition Author(s): Zhang, Y.Y., Xia, L.Y., Zhou, Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9KR9

This is version 1.0 of the entry. See complete history.

Literature

Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5

Zhang, Y.Y., Xia, L.Y., Zhou, Q.

To be published.

Macromolecule Content

Total Structure Weight: 468.59 kDa
Atom Count: 28,851
Modeled Residue Count: 3,552
Deposited Residue Count: 4,056
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B [auth C], C [auth B]	1,352	Pipistrellus bat coronavirus HKU5	Mutation(s): 2 Gene Names: S, 2
UniProt
Find proteins for A3EXD0 (Bat coronavirus HKU5) Explore A3EXD0 Go to UniProtKB: A3EXD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3EXD0
Glycosylation
Glycosylation Sites: 19	Glycosylation Focus chain A Focus chain B [auth C] Focus chain C [auth B]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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], E, F, H, I, J, K, L, M, N, O, Q, R, S, T, U, V, W, 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 E Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V Focus chain W 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 E Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain Q Focus chain R Focus chain S Focus chain T 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: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, P, Y	3		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: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLM (Subject of Investigation/LOI) Query on PLM Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain EA [auth A] SDF format, chain AB [auth B] MOL2 format, chain PA [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain AB [auth B] mmCIF format, chain PA [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain AB [auth B]	AB [auth B], EA [auth A], PA [auth C]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain EA [auth A] Focus chain PA [auth C] Interactions & Density Focus chain AB [auth B] Focus chain EA [auth A] Focus chain PA [auth C]
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 TA [auth C] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain OA [auth A] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain LA [auth A] SDF format, chain KB [auth B] SDF format, chain KA [auth A] SDF format, chain JB [auth B] SDF format, chain JA [auth A] SDF format, chain IB [auth B] SDF format, chain IA [auth A] SDF format, chain HB [auth B] SDF format, chain HA [auth A] SDF format, chain GB [auth B] SDF format, chain GA [auth A] SDF format, chain FB [auth B] SDF format, chain FA [auth A] SDF format, chain EB [auth B] SDF format, chain DB [auth B] SDF format, chain CB [auth B] SDF format, chain BB [auth B] 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 TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain OA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain BB [auth B] 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 TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain OA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain BB [auth B]	BB [auth B] CB [auth B] DB [auth B] EB [auth B] FA [auth A] BB [auth B], CB [auth B], DB [auth B], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], HA [auth A], HB [auth B], IA [auth A], IB [auth B], JA [auth A], JB [auth B], KA [auth A], KB [auth B], LA [auth A], MA [auth A], NA [auth A], OA [auth A], QA [auth C], RA [auth C], SA [auth C], TA [auth C], 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 B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] 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 B] Focus chain CB [auth B] Focus chain DB [auth B] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] 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]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	G, P, Y	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain G Focus chain P Focus chain Y Interactions & Density Focus chain G Focus chain P Focus chain Y

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.6.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82241081

Revision History (Full details and data files)

Version 1.0: 2025-11-05
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.