9J62 | pdb_00009j62

Cryo-EM structure of Bat SARS-like coronavirus Khosta-2 spike protein in complex with human ACE2 (local refined)

• PDB DOI: https://doi.org/10.2210/pdb9J62/pdb
• EM Map EMD-61159: EMDB EMDataResource

• Classification: VIRAL PROTEIN/HYDROLASE
• Organism(s): Homo sapiens, Bat SARS-like coronavirus Khosta-2
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-08-14 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

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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.

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: 94.2 kDa 
• Atom Count: 6,428 
• Modeled Residue Count: 786 
• Deposited Residue Count: 809 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Processed angiotensin-converting enzyme 2	A	605	Homo sapiens	Mutation(s): 0  Gene Names: ACE2, UNQ868/PRO1885 EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens) Explore Q9BYF1  Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1 GTEx:  ENSG00000130234
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q9BYF1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	204	Bat SARS-like coronavirus Khosta-2	Mutation(s): 0  Gene Names: S
UniProt
Find proteins for A0A8E6HRK4 (Bat SARS-like coronavirus Khosta-2) Explore A0A8E6HRK4  Go to UniProtKB:  A0A8E6HRK4
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], F [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.76 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Pan, X.Q., Li, L.J., Liu, K.F., Qi, J.X., Gao, G.F.

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

Revision History  

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