7E3J | pdb_00007e3j

Crystal structure of SARS-CoV-2 RBD binding to dog ACE2

• PDB DOI: https://doi.org/10.2210/pdb7E3J/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Canis lupus familiaris, Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli K-12, Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2021-02-08 Released: 2021-04-07 
• Deposition Author(s): Zhang, Z., Zhang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free: 
  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

The molecular basis for SARS-CoV-2 binding to dog ACE2.

Zhang, Z., Zhang, Y., Liu, K., Li, Y., Lu, Q., Wang, Q., Zhang, Y., Wang, L., Liao, H., Zheng, A., Ma, S., Fan, Z., Li, H., Huang, W., Bi, Y., Zhao, X., Wang, Q., Gao, G.F., Xiao, H., Tong, Z., Qi, J., Sun, Y.

(2021) Nat Commun 12: 4195-4195

• PubMed: 34234119 
• DOI: https://doi.org/10.1038/s41467-021-24326-y
• Primary Citation Related Structures: 
  7E3J


• PubMed Abstract: 
  

  SARS-CoV-2 can infect many domestic animals, including dogs. Herein, we show that dog angiotensin-converting enzyme 2 (dACE2) can bind to the SARS-CoV-2 spike (S) protein receptor binding domain (RBD), and that both pseudotyped and authentic SARS-CoV-2 can infect dACE2-expressing cells. We solved the crystal structure of RBD in complex with dACE2 and found that the total number of contact residues, contact atoms, hydrogen bonds and salt bridges at the binding interface in this complex are slightly fewer than those in the complex of the RBD and human ACE2 (hACE2). This result is consistent with the fact that the binding affinity of RBD to dACE2 is lower than that of hACE2. We further show that a few important mutations in the RBD binding interface play a pivotal role in the binding affinity of RBD to both dACE2 and hACE2. Our work reveals a molecular basis for cross-species transmission and potential animal spread of SARS-CoV-2, and provides new clues to block the potential transmission chains of this virus.

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Organizational Affiliation: 
• CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
Shanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an, China.
Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
The Northern Medical District of the PLA General Hospital, Beijing, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. [e-mail].
Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. [e-mail].
Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China. [e-mail].

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: 106.42 kDa 
• Atom Count: 7,245 
• Modeled Residue Count: 890 
• Deposited Residue Count: 918 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE2	A	723	Canis lupus familiaris	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	B	195	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

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	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.256	α = 90
b = 168.256	β = 90
c = 211.196	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Zhang, Z., Zhang, Y.

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2021-07-28
  Changes: Source and taxonomy
• Version 1.3: 2021-08-25
  Changes: Database references, Structure summary
• Version 1.4: 2021-10-13
  Changes: Database references
• Version 1.5: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.6: 2024-11-13
  Changes: Structure summary