4ZTD

Crystal Structure of Human PCNA in complex with a TRAIP peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress.

Hoffmann, S.Smedegaard, S.Nakamura, K.Mortuza, G.B.Raschle, M.Ibanez de Opakua, A.Oka, Y.Feng, Y.Blanco, F.J.Mann, M.Montoya, G.Groth, A.Bekker-Jensen, S.Mailand, N.

(2016) J Cell Biol 212: 63-75

  • DOI: 10.1083/jcb.201506071
  • Primary Citation of Related Structures:  
    4ZTD

  • PubMed Abstract: 
  • Cellular genomes are highly vulnerable to perturbations to chromosomal DNA replication. Proliferating cell nuclear antigen (PCNA), the processivity factor for DNA replication, plays a central role as a platform for recruitment of genome surveillance and DNA repair factors to replication forks, allowing cells to mitigate the threats to genome stability posed by replication stress ...

    Cellular genomes are highly vulnerable to perturbations to chromosomal DNA replication. Proliferating cell nuclear antigen (PCNA), the processivity factor for DNA replication, plays a central role as a platform for recruitment of genome surveillance and DNA repair factors to replication forks, allowing cells to mitigate the threats to genome stability posed by replication stress. We identify the E3 ubiquitin ligase TRAIP as a new factor at active and stressed replication forks that directly interacts with PCNA via a conserved PCNA-interacting peptide (PIP) box motif. We show that TRAIP promotes ATR-dependent checkpoint signaling in human cells by facilitating the generation of RPA-bound single-stranded DNA regions upon replication stress in a manner that critically requires its E3 ligase activity and is potentiated by the PIP box. Consequently, loss of TRAIP function leads to enhanced chromosomal instability and decreased cell survival after replication stress. These findings establish TRAIP as a PCNA-binding ubiquitin ligase with an important role in protecting genome integrity after obstacles to DNA replication.


    Related Citations: 
    • Structure of p15(PAF)-PCNA complex and implications for clamp sliding during DNA replication and repair.
      De Biasio, A., de Opakua, A.I., Mortuza, G.B., Molina, R., Cordeiro, T.N., Castillo, F., Villate, M., Merino, N., Delgado, S., Gil-Carton, D., Luque, I., Diercks, T., Bernado, P., Montoya, G., Blanco, F.J.
      (2015) Nat Commun 6: 6439

    Organizational Affiliation

    Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark niels.mailand@cpr.ku.dk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenA, B, C253Homo sapiensMutation(s): 0 
Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
Explore P12004 
Go to UniProtKB:  P12004
PHAROS:  P12004
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-PHE-GLN-ALA-LYS-LEU-ASP-THR-PHE-LEU-TRP-SERD, E12Homo sapiensMutation(s): 0 
Gene Names: TRAIPRNF206TRIP
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWF2 (Homo sapiens)
Explore Q9BWF2 
Go to UniProtKB:  Q9BWF2
PHAROS:  Q9BWF2
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-GLY-ALA-GLY-ALAF5Homo sapiensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.36α = 90
b = 84.36β = 90
c = 210.862γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references