1U76

Crystal structure of hPCNA bound to residues 452-466 of the DNA polymerase-delta-p66 subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Thermodynamic Analysis of Human PCNA with Peptides Derived from DNA Polymerase-delta p66 Subunit and Flap Endonuclease-1.

Bruning, J.B.Shamoo, Y.

(2004) Structure 12: 2209-2219

  • DOI: 10.1016/j.str.2004.09.018
  • Primary Citation of Related Structures:  1U7B

  • PubMed Abstract: 
  • Human Proliferating Cellular Nuclear Antigen (hPCNA), a member of the sliding clamp family of proteins, makes specific protein-protein interactions with DNA replication and repair proteins through a small peptide motif termed the PCNA-interacting pro ...

    Human Proliferating Cellular Nuclear Antigen (hPCNA), a member of the sliding clamp family of proteins, makes specific protein-protein interactions with DNA replication and repair proteins through a small peptide motif termed the PCNA-interacting protein, or PIP-box. We solved the structure of hPCNA bound to PIP-box-containing peptides from the p66 subunit of the human replicative DNA polymerase-delta (452-466) at 2.6 A and of the flap endonuclease (FEN1) (331-350) at 1.85 A resolution. Both structures demonstrate that the pol-delta p66 and FEN1 peptides interact with hPCNA at the same site shown to bind the cdk-inhibitor p21(CIP1). Binding studies indicate that peptides from the p66 subunit of the pol-delta holoenzyme and FEN1 bind hPCNA from 189- to 725-fold less tightly than those of p21. Thus, the PIP-box and flanking regions provide a small docking peptide whose affinities can be readily adjusted in accord with biological necessity to mediate the binding of DNA replication and repair proteins to hPCNA.


    Organizational Affiliation

    Department of Biochemistry and Cell Biology, Rice University, 6100 South Main Street, MS140, Houston, TX 77005, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, C, E
261Homo sapiensGene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to Gene View: PCNA
Go to UniProtKB:  P12004
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
KANRQVSITGFFQRK peptide from DNA polymerase delta subunit 3
B, D, F
15Homo sapiensGene Names: POLD3 (KIAA0039)
Find proteins for Q15054 (Homo sapiens)
Go to Gene View: POLD3
Go to UniProtKB:  Q15054
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 82.480α = 90.00
b = 82.480β = 90.00
c = 203.800γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance