8Q7I

PCNA from Chaetomium thermophilum in complex with Fen1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Canonical binding of Chaetomium thermophilum DNA polymerase delta / zeta subunit PolD3 and flap endonuclease Fen1 to PCNA.

Alphey, M.S.Wolford, C.B.MacNeill, S.A.

(2023) Front Mol Biosci 10: 1320648-1320648

  • DOI: https://doi.org/10.3389/fmolb.2023.1320648
  • Primary Citation of Related Structures:  
    8P9O, 8Q7I

  • PubMed Abstract: 

    The sliding clamp PCNA is a key player in eukaryotic genome replication and stability, acting as a platform onto which components of the DNA replication and repair machinery are assembled. Interactions with PCNA are frequently mediated via a short protein sequence motif known as the PCNA-interacting protein (PIP) motif. Here we describe the binding mode of a PIP motif peptide derived from C-terminus of the PolD3 protein from the thermophilic ascomycete fungus C. thermophilum , a subunit of both DNA polymerase δ (Pol δ) and the translesion DNA synthesis polymerase Pol ζ, characterised by isothermal titration calorimetry (ITC) and protein X-ray crystallography. In sharp contrast to the previously determined structure of a Chaetomium thermophilum PolD4 peptide bound to PCNA, binding of the PolD3 peptide is strictly canonical, with the peptide adopting the anticipated 3 10 helix structure, conserved Gln441 inserting into the so-called Q-pocket on PCNA, and Ile444 and Phe448 forming a two-fork plug that inserts into the hydrophobic surface pocket on PCNA. The binding affinity for the canonical PolD3 PIP-PCNA interaction determined by ITC is broadly similar to that previously determined for the non-canonical PolD4 PIP-PCNA interaction. In addition, we report the structure of a PIP peptide derived from the C. thermophilum Fen1 nuclease bound to PCNA. Like PolD3, Fen1 PIP peptide binding to PCNA is achieved by strictly canonical means. Taken together, these results add to an increasing body of information on how different proteins bind to PCNA, both within and across species.


  • Organizational Affiliation

    Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen262Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0061010
UniProt
Find proteins for G0SF70 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SF70 
Go to UniProtKB:  G0SF70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0SF70
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Flap endonuclease 1B [auth P]15Thermochaetoides thermophila DSM 1495Mutation(s): 0 
EC: 3.1
UniProt
Find proteins for G0S2B5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S2B5 
Go to UniProtKB:  G0S2B5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S2B5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.354α = 90
b = 87.354β = 90
c = 214.333γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Carnegie Trust for the Universities of ScotlandUnited Kingdom70668

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Database references