5HOG

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Dna2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase.

Villa, F.Simon, A.C.Ortiz Bazan, M.A.Kilkenny, M.L.Wirthensohn, D.Wightman, M.Matak-Vinkovic, D.Pellegrini, L.Labib, K.

(2016) Mol Cell 63: 385-396

  • DOI: https://doi.org/10.1016/j.molcel.2016.06.009
  • Primary Citation of Related Structures:  
    5HOG, 5HOI

  • PubMed Abstract: 

    Replisome assembly at eukaryotic replication forks connects the DNA helicase to DNA polymerases and many other factors. The helicase binds the leading-strand polymerase directly, but is connected to the Pol α lagging-strand polymerase by the trimeric adaptor Ctf4. Here, we identify new Ctf4 partners in addition to Pol α and helicase, all of which contain a "Ctf4-interacting-peptide" or CIP-box. Crystallographic analysis classifies CIP-boxes into two related groups that target different sites on Ctf4. Mutations in the CIP-box motifs of the Dna2 nuclease or the rDNA-associated protein Tof2 do not perturb DNA synthesis genome-wide, but instead lead to a dramatic shortening of chromosome 12 that contains the large array of rDNA repeats. Our data reveal unexpected complexity of Ctf4 function, as a hub that connects multiple accessory factors to the replisome. Most strikingly, Ctf4-dependent recruitment of CIP-box proteins couples other processes to DNA synthesis, including rDNA copy-number regulation.


  • Organizational Affiliation

    MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase alpha-binding protein
A, B, C
478Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF4CHL15POB1YPR135WP9659.7
UniProt
Find proteins for Q01454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01454 
Go to UniProtKB:  Q01454
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01454
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dna2p
D, E
17Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.1 (UniProt), 3.6.4.12 (UniProt)
UniProt
Find proteins for P38859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38859 
Go to UniProtKB:  P38859
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38859
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.677α = 90
b = 99.551β = 90
c = 218.373γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z
Gates Cambridge PhD programUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references