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)

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Experimental Data Snapshot

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

Literature

Molecular Insights into Species-Specific ACE2 Recognition of Coronavirus HKU5

Zhang, Y.Y., Xia, L.Y., Zhou, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

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

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
Glycosylation
Glycosylation Sites: 2

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
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Zhang, Y.Y., Xia, L.Y., Zhou, Q.

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

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release