3L10

Structure of split monoubiquitinated PCNA with ubiquitin in position one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of monoubiquitinated PCNA and implications for translesion synthesis and DNA polymerase exchange.

Freudenthal, B.D.Gakhar, L.Ramaswamy, S.Washington, M.T.

(2010) Nat Struct Mol Biol 17: 479-484

  • DOI: https://doi.org/10.1038/nsmb.1776
  • Primary Citation of Related Structures:  
    3L0W, 3L0X, 3L10

  • PubMed Abstract: 

    DNA synthesis by classical polymerases can be blocked by many lesions. These blocks are overcome by translesion synthesis, whereby the stalled classical, replicative polymerase is replaced by a nonclassical polymerase. In eukaryotes this polymerase exchange requires proliferating cell nuclear antigen (PCNA) monoubiquitination. To better understand the polymerase exchange, we developed a means of producing monoubiquitinated PCNA, by splitting the protein into two self-assembling polypeptides. We determined the X-ray crystal structure of monoubiquitinated PCNA and found that the ubiquitin moieties are located on the back face of PCNA and interact with it through their canonical hydrophobic surface. Moreover, the attachment of ubiquitin does not change PCNA's conformation. We propose that PCNA ubiquitination facilitates nonclassical polymerase recruitment to the back of PCNA by forming a new binding surface for nonclassical polymerases, consistent with a 'tool belt' model of the polymerase exchange.


  • Organizational Affiliation

    Department of Biochemistry, University of Iowa College of Medicine, Iowa City, Iowa, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen169Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL30YBR0811YBR088C
UniProt
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15873 
Go to UniProtKB:  P15873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15873
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Monoubiquitinated Proliferating cell nuclear antigen169Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL30Pol30 & UBI1YBR0811YBR088C
UniProt
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05759 
Go to UniProtKB:  P05759
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15873 
Go to UniProtKB:  P15873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP15873P05759
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.277 
  • R-Value Observed: 0.279 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.516α = 90
b = 122.516β = 90
c = 122.516γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-02
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Refinement description