7YEQ | pdb_00007yeq

Structural insight into African Swine Fever Virus CP312R protein reveals it as a single-stranded DNA binding protein

• PDB DOI: https://doi.org/10.2210/pdb7YEQ/pdb

• Classification: VIRUS
• Organism(s): African swine fever virus
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2022-07-06 Released: 2023-07-26 
• Deposition Author(s): Chen, L.F., Wu, Y.K.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.258 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Structural insights into the CP312R protein of the African swine fever virus.

Chen, L., Chen, L., Chen, H., Zhang, H., Dong, P., Sun, L., Huang, X., Lin, P., Wu, L., Jing, D., Qian, Y., Wu, Y.

(2022) Biochem Biophys Res Commun 624: 68-74

• PubMed: 35933928 
• DOI: https://doi.org/10.1016/j.bbrc.2022.07.091
• Primary Citation of Related Structures:  
  7YEQ


• PubMed Abstract: 
  

  African swine fever (ASF) is a lethal hemorrhagic disease that affects domestic pigs and wild boars. There is no medication available for ASF to date. The ability to mount antigen-specific responses to viral vectored CP312R makes it a crucial potential target for designing vaccines or drugs. This study determined the crystal structure of ASFV CP312R at 2.32 Å and found it to be a monomer with a single-stranded DNA binding core domain with a clear five-strands β-barrel OB-fold architecture. Electrophoretic mobility shift assay and size-exclusion chromatography characterization assay further confirmed the single-stranded DNA (ssDNA)-binding property of ASFV CP312R. This study revealed the structure and preliminary ssDNA interaction mechanisms of ASFV CP312R, providing new clues for developing new antiviral strategies.

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Organizational Affiliation: 
• Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].
MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu Province, China. Electronic address: [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation & Fujian Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 34.53 kDa 
• Atom Count: 2,219 
• Modeled Residue Count: 274 
• Deposited Residue Count: 307 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CP312R	A	307	African swine fever virus	Mutation(s): 0  Gene Names: CP312R CDS, ASFV-Georgia_4-120, CP312R
UniProt
Find proteins for A0A2X0RVH4 (African swine fever virus) Explore A0A2X0RVH4  Go to UniProtKB:  A0A2X0RVH4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.258 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.172	α = 90
b = 66.608	β = 90
c = 115.099	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Chen, L.F., Wu, Y.K.

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Funding Organization	Location	Grant Number
Other government	China	National Natural Science Foundation of China (32002049)

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 1.2: 2025-02-26
  Changes: Database references, Structure summary