3AIZ

Crystal structure of PCNA2-PCNA3 complex from Sulfolobus tokodaii (P21212)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

A novel heterotetrameric structure of the crenarchaeal PCNA2-PCNA3 complex

Kawai, A., Hashimoto, H., Higuchi, S., Tsunoda, M., Sato, M., Nakamura, K.T., Miyamoto, S.

(2011) J.Struct.Biol. 174: 443-450

  • DOI: 10.1016/j.jsb.2011.02.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Proliferating cell nuclear antigen (PCNA) is a key protein that orchestrates the arrangement of DNA-processing proteins on DNA during DNA metabolism. In crenarchaea, PCNA forms a heterotrimer (PCNA123) consisting of PCNA1, PCNA2, and PCNA3, while in ...

    Proliferating cell nuclear antigen (PCNA) is a key protein that orchestrates the arrangement of DNA-processing proteins on DNA during DNA metabolism. In crenarchaea, PCNA forms a heterotrimer (PCNA123) consisting of PCNA1, PCNA2, and PCNA3, while in most eukaryotes and many archaea PCNAs form a homotrimer. Interestingly, unique oligomeric PCNAs from Sulfolobus tokodaii were reported in which PCNA2 and PCNA3 form a heterotrimer without PCNA1. In this paper, we describe the crystal structure of the stoPCNA2-stoPCNA3 complex. While most DNA sliding clamps form ring-shaped structures, our crystal structure showed an elliptic ring-like heterotetrameric complex, differing from a previous reports. Furthermore, we investigated the composition and the dimension of the stoPCNA2-stoPCNA3 complex in the solution using gel-filtration column chromatography and small-angle X-ray scattering analyses, respectively. These results indicate that stoPCNA2 and stoPCNA3 form the heterotetramer in solution. Based on our heterotetrameric structure, we propose a possible biological role for the heterotetrameric complex as a Holliday junction clamp.

    Organizational Affiliation: 

    Sojo University, Ikeda, Kumamoto, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase sliding clamp B
A, B
248Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)Mutation(s): 0 
Gene Names: pcn2 (pcnB)
Find proteins for Q975M2 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q975M2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase sliding clamp C
C, D
246Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)Mutation(s): 0 
Gene Names: pcn3 (pcnC)
Find proteins for Q973F5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q973F5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.110α = 90.00
b = 160.570β = 90.00
c = 116.560γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance