9KUD | pdb_00009kud

Crystal structure of SARS-CoV-2 JN.1 variant RBD complexed with squirrel ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 
    0.281 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Cross-species recognition of squirrel ACE2 by the receptor binding domains of SARS-CoV-2, RaTG13, PCoV-GD and PCoV-GX.

Wang, C.Nan, X.Deng, Y.Fan, S.Lan, J.

(2025) Structure 33: 1750

  • DOI: https://doi.org/10.1016/j.str.2025.07.003
  • Primary Citation Related Structures: 
    9JR4, 9JR5, 9JR7, 9JRC, 9KUD

  • PubMed Abstract: 

    SARS-CoV-2 has a broad animal host range, but its origin and intermediate hosts are still debated. Arctic ground squirrel is proved to be a susceptible animal host of SARS-CoV-2 and RaTG13, as the Arctic ground squirrel ACE2 (sACE2) could bind to the RBDs of SARS-CoV-2 and RaTG13, and support transduction of the SARS-CoV-2 and RaTG13 pseudovirions. Here, we determined crystal structures of sACE2 bound to the RBDs of RaTG13, PCoV-GD, PCoV-GX, SARS-CoV-2 A372T and SARS-CoV-2 JN.1 variant. SPR assay indicated that RBD residues 493, 498 and 501 might be important for sACE2 recognition. Notably, N322-linked glycans of sACE2 were found to be in contact with S375 of the RaTG13 RBD. Moreover, the recent SARS-CoV-2 KP.2 and KP.3 variant RBDs could also bind to the sACE2. Our results provide further insights into interactions between coronavirus RBD and cell receptor ACE2, which may promote our understanding of SARS-CoV-2 evolution.


  • Organizational Affiliation
    • School of Biomedical Sciences, Hunan University, Changsha, Hunan, China.

Macromolecule Content 

  • Total Structure Weight: 185.99 kDa 
  • Atom Count: 12,990 
  • Modeled Residue Count: 1,575 
  • Deposited Residue Count: 1,586 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme
A, B
596Petaurus norfolcensisMutation(s): 0 
Gene Names: ACE2
EC: 3.4 (PDB Primary Data), 3.4.17 (UniProt), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8R0I0 (Mus musculus)
Explore Q8R0I0 
Go to UniProtKB:  Q8R0I0
IMPC:  MGI:1917258
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R0I0
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q8R0I0-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike protein S1C [auth E],
D [auth F]
197Severe acute respiratory syndrome coronavirus 2Mutation(s): 18 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE [auth C]4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
K [auth E]
L [auth E]
F [auth A],
G [auth A],
H [auth A],
K [auth E],
L [auth E],
M [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
I [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free:  0.281 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.674α = 90
b = 129.157β = 90
c = 138.062γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references
  • Version 1.2: 2025-10-22
    Changes: Database references