3LX1

Crystal Structure analysis of PCNA1 from Thermococcus kodakaraensis tk0535


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis.

Ladner, J.E.Pan, M.Hurwitz, J.Kelman, Z.

(2011) Proc Natl Acad Sci U S A 108: 2711-2716

  • DOI: https://doi.org/10.1073/pnas.1019179108
  • Primary Citation of Related Structures:  
    3LX1, 3LX2

  • PubMed Abstract: 

    Proliferating cell nuclear antigen (PCNA) is a ring-shaped protein that encircles duplex DNA and plays an essential role in many DNA metabolic processes in archaea and eukarya. The eukaryotic and euryarchaea genomes contain a single gene encoding for PCNA. Interestingly, the genome of the euryarchaeon Thermococcus kodakaraensis contains two PCNA-encoding genes (TK0535 and TK0582), making it unique among the euryarchaea kingdom. It is shown here that the two T. kodakaraensis PCNA proteins support processive DNA synthesis by the polymerase. Both proteins form trimeric structures with characteristics similar to those of other archaeal and eukaryal PCNA proteins. One of the notable differences between the TK0535 and TK0582 rings is that the interfaces are different, resulting in different stabilities for the two trimers. The possible implications of these observations for PCNA functions are discussed.


  • Organizational Affiliation

    National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase sliding clamp 1255Thermococcus kodakarensisMutation(s): 0 
Gene Names: pcn1TK0535
UniProt
Find proteins for Q5JF32 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JF32 
Go to UniProtKB:  Q5JF32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JF32
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.23α = 90
b = 89.23β = 90
c = 62.67γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-06-20
    Changes: Database references
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations