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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 9J62

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

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BYF1
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A	Go to GlyGen: Q9BYF1-1
Sequence Annotations Expand
Reference Sequence

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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

Small Molecules

Ligands 2 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 G [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	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		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-20

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-08-20
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.