2ZVV

Crystal structure of Proliferating cellular nuclear antigen 1 and Short peptide from human P21


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the Arabidopsis thaliana proliferating cell nuclear antigen 1 and 2 proteins complexed with the human p21 C-terminal segment

Strzalka, W.Oyama, T.Tori, K.Morikawa, K.

(2009) Protein Sci 18: 1072-1080

  • DOI: https://doi.org/10.1002/pro.117
  • Primary Citation of Related Structures:  
    2ZVV, 2ZVW

  • PubMed Abstract: 

    The proliferating cell nuclear antigen (PCNA) is well recognized as one of the essential cellular components of the DNA replication machinery in all eukaryotic organisms. Despite their prominent importance, very little biochemical and structural information about plant PCNAs is available, in comparison with that obtained from other eukaryotic organisms. We have determined the atomic resolution crystal structures of the two distinct Arabidopsis thaliana PCNAs (AtPCNA), both complexed with the C-terminal segment of human p21. Both AtPCNAs form homotrimeric ring structures, which are essentially identical to each other, including the major contacts with the p21 peptide. The structure of the amino-terminal half of the p21 peptide, containing the typical PIP box sequence, is remarkably similar to those observed in the previously reported crystal structures of the human and archaeal PCNA-PIP box complexes. Meanwhile, the carboxy-terminal halves of the p21 peptide in the plant PCNA complexes are bound to the protein in a unique manner, most probably because of crystal packing effects. A surface plasmon resonance analysis revealed high affinity between each AtPCNA and the C-terminal fragment of human p21. This result strongly suggests that the interaction is functionally significant, although no plant homologs of p21 have been identified yet. We also discovered that AtPCNA1 and AtPCNA2 form heterotrimers, implying that hetero-PCNA rings may play critical roles in cellular signal transduction, particularly in DNA repair.


  • Organizational Affiliation

    Department of Molecular Genetics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cellular nuclear antigen 1
A, B
276Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9M7Q7 (Arabidopsis thaliana)
Explore Q9M7Q7 
Go to UniProtKB:  Q9M7Q7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M7Q7
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase inhibitor 1C [auth Y],
D [auth X]
22N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P38936 (Homo sapiens)
Explore P38936 
Go to UniProtKB:  P38936
PHAROS:  P38936
GTEx:  ENSG00000124762 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38936
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.232 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.01α = 90
b = 111.01β = 90
c = 403.903γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description