4CS5

Crystal Structure of PCNA from Litopenaeus vannamei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


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Literature

Crystal Structure of the Shrimp Proliferating Cell Nuclear Antigen: Structural Complementarity with Wssv DNA Polymerase Pip-Box.

Carrasco-Miranda, J.S.Lopez-Zavala, A.A.Arvizu-Flores, A.A.Garcia-Orozco, K.D.Stojanoff, V.Rudino-Pinera, E.Brieba, L.G.Sotelo-Mundo, R.R.

(2014) Plos One 9: 94369

  • DOI: 10.1371/journal.pone.0094369

  • PubMed Abstract: 
  • DNA replication requires processivity factors that allow replicative DNA polymerases to extend long stretches of DNA. Some DNA viruses encode their own replicative DNA polymerase, such as the white spot syndrome virus (WSSV) that infects decapod crus ...

    DNA replication requires processivity factors that allow replicative DNA polymerases to extend long stretches of DNA. Some DNA viruses encode their own replicative DNA polymerase, such as the white spot syndrome virus (WSSV) that infects decapod crustaceans but still require host replication accessory factors. We have determined by X-ray diffraction the three-dimensional structure of the Pacific white leg shrimp Litopenaeus vannamei Proliferating Cell Nuclear Antigen (LvPCNA). This protein is a member of the sliding clamp family of proteins, that binds DNA replication and DNA repair proteins through a motif called PIP-box (PCNA-Interacting Protein). The crystal structure of LvPCNA was refined to a resolution of 3 Å, and allowed us to determine the trimeric protein assembly and details of the interactions between PCNA and the DNA. To address the possible interaction between LvPCNA and the viral DNA polymerase, we docked a theoretical model of a PIP-box peptide from the WSSV DNA polymerase within LvPCNA crystal structure. The theoretical model depicts a feasible model of interaction between both proteins. The crystal structure of shrimp PCNA allows us to further understand the mechanisms of DNA replication processivity factors in non-model systems.


    Related Citations: 
    • Crystallization and X-Ray Diffraction Studies of Crustacean Proliferating Cell Nuclear Antigen.
      Carrasco-Miranda, J.S.,Cardona-Felix, C.S.,Lopez-Zavala, A.A.,De-La-Re-Vega, E.,De La Mora, E.,Rudino-Pinera, E.,Sotelo-Mundo, R.R.,Brieba, L.G.
      (2012) Acta Crystallogr.,Sect.F 68: 1367


    Organizational Affiliation

    Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, México.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROLIFERATING CELL NUCLEAR ANTIGEN
A, B, C
260Penaeus vannameiMutation(s): 0 
Gene Names: PCNA
Find proteins for G1E6N7 (Penaeus vannamei)
Go to Gene View: PCNA
Go to UniProtKB:  G1E6N7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.265 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.570α = 90.00
b = 83.380β = 117.65
c = 74.310γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release