9KRA | pdb_00009kra

The RBD of HKU5 complex with Pipistrellus abramus ACE2

PDB DOI: https://doi.org/10.2210/pdb9KRA/pdb
EM Map EMD-62524: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pipistrellus bat coronavirus HKU5, Pipistrellus abramus
Expression System: Homo sapiens
Mutation(s): No

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 9KRA

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: 118.11 kDa
Atom Count: 6,607
Modeled Residue Count: 789
Deposited Residue Count: 1,002
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	199	Pipistrellus bat coronavirus HKU5	Mutation(s): 0 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: 2	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	B	803	Pipistrellus abramus	Mutation(s): 0 EC: 3.4
UniProt
Find proteins for C7ECT9 (Pipistrellus abramus) Explore C7ECT9 Go to UniProtKB: C7ECT9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7ECT9
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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	C, D, E, F, G C, D, E, F, G, H	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	I [auth A], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B]

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.