7W6R | pdb_00007w6r

Structure of Bat coronavirus RaTG13 spike receptor-binding domain complexed with its receptor equine ACE2

• PDB DOI: https://doi.org/10.2210/pdb7W6R/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Equus caballus, Bat coronavirus RaTG13
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2021-12-02 Released: 2022-06-08 
• Deposition Author(s): Xu, Z.P., Liu, K.F., Han, P., Qi, J.X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Binding and structural basis of equine ACE2 to RBDs from SARS-CoV, SARS-CoV-2 and related coronaviruses

Xu, Z., Kang, X., Han, P., Du, P., Li, L., Zheng, A., Deng, C., Qi, J., Zhao, X., Wang, Q., Liu, K., Gao, G.F.

(2022) Nat Commun 13: 3547

• DOI: https://doi.org/10.1038/s41467-022-31276-6

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 95.21 kDa 
• Atom Count: 6,591 
• Modeled Residue Count: 792 
• Deposited Residue Count: 825 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiotensin-converting enzyme	A	602	Equus caballus	Mutation(s): 0  Gene Names: ACE2 EC: 3.4
UniProt
Find proteins for A0A9L0TPT7 (Equus caballus) Explore A0A9L0TPT7  Go to UniProtKB:  A0A9L0TPT7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	223	Bat coronavirus RaTG13	Mutation(s): 0
UniProt
Find proteins for A0ABF7PLN6 (Bat coronavirus RaTG13) Explore A0ABF7PLN6  Go to UniProtKB:  A0ABF7PLN6
Glycosylation
Glycosylation Sites: 1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.782	α = 90
b = 122.837	β = 92.42
c = 68.797	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Xu, Z.P., Liu, K.F., Han, P., Qi, J.X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100752

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2022-12-21
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary