6KI3

The crystal structure of AsfvAP:dF commplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report



Literature

A unique DNA-binding mode of African swine fever virus AP endonuclease.

Chen, Y.Chen, X.Huang, Q.Shao, Z.Gao, Y.Li, Y.Yang, C.Liu, H.Li, J.Wang, Q.Ma, J.Zhang, Y.Z.Gu, Y.Gan, J.

(2020) Cell Discov 6: 13-13

  • DOI: 10.1038/s41421-020-0146-2
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. ASFV is primarily replicated in the cytoplasm of pig macrophages, which is oxidative and caused constant damage to ASFV genome. ASFV AP endonuclease ( Asfv ...

    African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. ASFV is primarily replicated in the cytoplasm of pig macrophages, which is oxidative and caused constant damage to ASFV genome. ASFV AP endonuclease ( Asfv AP) catalyzes DNA cleavage reaction at the abasic site and is a key enzyme of ASFV base excision repair (BER) system. Although it plays an essential role in ASFV survival in host cells, the basis underlying substrate binding and cleavage by Asfv AP remains unclear. Here, we reported the structural and functional studies of Asfv AP, showing that Asfv AP adopts a novel DNA-binding mode distinct from other APs. Asfv AP possesses many unique structural features, including one narrower nucleotide-binding pocket at the active site, the C16-C20 disulfide bond-containing region, and histidine-rich loop. As indicated by our mutagenesis, in vitro binding and cleavage assays, these features are important for Asfv AP to suit the acidic and oxidative environment. Owing to their functional importance, these unique features could serve as targets for designing small molecule inhibitors that could disrupt the repair process of ASFV genome and help fight against this deadly virus in the future.


    Organizational Affiliation

    1State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable AP endonuclease
A, B
301African swine fever virus tick/South Africa/Pretoriuskop Pr4/1996Mutation(s): 0 
Gene Names: Pret-146
EC: 3.1.21
Find proteins for P0C9C6 (African swine fever virus (isolate Tick/South Africa/Pretoriuskop Pr4/1996))
Go to UniProtKB:  P0C9C6
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*AP*GP*CP*GP*TP*CP*C)-3')C, F9African swine fever virus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*AP*G)-3')D, G8African swine fever virus
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*CP*TP*G)-3')E, H17African swine fever virus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.637α = 90
b = 84.698β = 93.66
c = 98.585γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
HKL2Mapphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-07-17 
  • Released Date: 2020-05-27 
  • Deposition Author(s): Chen, Y., Gan, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31370728

Revision History 

  • Version 1.0: 2020-05-27
    Type: Initial release