9JR4 | pdb_00009jr4

Crystal structure of RaTG13 receptor-binding domain complexed with squirrel ACE2

• PDB DOI: https://doi.org/10.2210/pdb9JR4/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Petaurus norfolcensis, Bat coronavirus RaTG13
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2024-09-29 Released: 2025-08-06 
• Deposition Author(s): Lan, J., Nan, X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free: 
  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

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 

• DOI: https://doi.org/10.1016/j.str.2025.07.003

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.23 kDa 
• Atom Count: 6,557 
• Modeled Residue Count: 786 
• Deposited Residue Count: 795 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A [auth B]	597	Petaurus norfolcensis	Mutation(s): 0  Gene Names: ACE2 EC: 3.4
UniProt
Find proteins for A0A8D2KIZ1 (Urocitellus parryii) Explore A0A8D2KIZ1  Go to UniProtKB:  A0A8D2KIZ1
Glycosylation
Glycosylation Sites: 4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B [auth E]	198	Bat coronavirus RaTG13	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth A]	5		N-Glycosylation

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B], G [auth B], H [auth B], J [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.76 Å
• R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.99	α = 90
b = 168.99	β = 90
c = 86.08	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Lan, J., Nan, X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release