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 1.3 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: 10.1038/nsmb.1776
  • Structures With Same Primary Citation

  • 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 e ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigenA169Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL30YBR0811YBR088C
Find proteins for P15873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P15873 
Go to UniProtKB:  P15873
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Monoubiquitinated Proliferating cell nuclear antigenB169Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: POL30Pol30 & UBI1YBR0811YBR088C
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
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • 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

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Entry History 

Deposition Data

Revision History 

  • 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