6GWS

Crystal structure of human PCNA in complex with three p15 peptides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

p15PAF binding to PCNA modulates the DNA sliding surface.

De March, M.Barrera-Vilarmau, S.Crespan, E.Mentegari, E.Merino, N.Gonzalez-Magana, A.Romano-Moreno, M.Maga, G.Crehuet, R.Onesti, S.Blanco, F.J.De Biasio, A.

(2018) Nucleic Acids Res. 46: 9816-9828

  • DOI: 10.1093/nar/gky723
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the ...

    p15PAF is an oncogenic intrinsically disordered protein that regulates DNA replication and lesion bypass by interacting with the human sliding clamp PCNA. In the absence of DNA, p15PAF traverses the PCNA ring via an extended PIP-box that contacts the sliding surface. Here, we probed the atomic-scale structure of p15PAF-PCNA-DNA ternary complexes. Crystallography and MD simulations show that, when p15PAF occupies two subunits of the PCNA homotrimer, DNA within the ring channel binds the unoccupied subunit. The structure of PCNA-bound p15PAF in the absence and presence of DNA is invariant, and solution NMR confirms that DNA does not displace p15PAF from the ring wall. Thus, p15PAF reduces the available sliding surfaces of PCNA, and may function as a belt that fastens the DNA to the clamp during synthesis by the replicative polymerase (pol δ). This constraint, however, may need to be released for efficient DNA lesion bypass by the translesion synthesis polymerase (pol η). Accordingly, our biochemical data show that p15PAF impairs primer synthesis by pol η-PCNA holoenzyme against both damaged and normal DNA templates. In light of our findings, we discuss the possible mechanistic roles of p15PAF in DNA replication and suppression of DNA lesion bypass.


    Organizational Affiliation

    Institute of Molecular Genetics, IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy.,Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy.,CIC bioGUNE, Parque Tecnológico de Bizkaia Edificio 800, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.,Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain.,Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, B, C
264Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to Gene View: PCNA
Go to UniProtKB:  P12004
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PCNA-associated factor
D, E, F
32Homo sapiensMutation(s): 0 
Gene Names: PCLAF (KIAA0101, NS5ATP9, PAF)
Find proteins for Q15004 (Homo sapiens)
Go to Gene View: PCLAF
Go to UniProtKB:  Q15004
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.240α = 90.00
b = 89.750β = 117.25
c = 85.130γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainCTQ2017-83810-R

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-09-05
    Type: Data collection, Database references
  • Version 1.2: 2018-10-24
    Type: Data collection, Database references