9KRB | pdb_00009krb

The RBD of HKU5 complex with Pitta sordida ACE2

PDB DOI: https://doi.org/10.2210/pdb9KRB/pdb
EM Map EMD-62525: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pipistrellus bat coronavirus HKU5, Pitta sordida
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: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9KRB

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: 113.18 kDa
Atom Count: 6,587
Modeled Residue Count: 796
Deposited Residue Count: 969
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	770	Pitta sordida	Mutation(s): 0 Gene Names: Ace2, PITSOR_R11116 EC: 3.4
UniProt
Find proteins for A0A851FF99 (Pitta sordida) Explore A0A851FF99 Go to UniProtKB: A0A851FF99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A851FF99
Glycosylation
Glycosylation Sites: 4	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	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G
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 H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.22 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.6.0

Structure Validation

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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.