5NXQ

Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to a stapled Sld5 CIP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Targeting the Genome-Stability Hub Ctf4 by Stapled-Peptide Design.

Wu, Y.Villa, F.Maman, J.Lau, Y.H.Dobnikar, L.Simon, A.C.Labib, K.Spring, D.R.Pellegrini, L.

(2017) Angew Chem Int Ed Engl 56: 12866-12872

  • DOI: https://doi.org/10.1002/anie.201705611
  • Primary Citation of Related Structures:  
    5NXQ

  • PubMed Abstract: 

    The exploitation of synthetic lethality by small-molecule targeting of pathways that maintain genomic stability is an attractive chemotherapeutic approach. The Ctf4/AND-1 protein hub, which links DNA replication, repair, and chromosome segregation, represents a novel target for the synthetic lethality approach. Herein, we report the design, optimization, and validation of double-click stapled peptides encoding the Ctf4-interacting peptide (CIP) of the replicative helicase subunit Sld5. By screening stapling positions in the Sld5 CIP, we identified an unorthodox i,i+6 stapled peptide with improved, submicromolar binding to Ctf4. The mode of interaction with Ctf4 was confirmed by a crystal structure of the stapled Sld5 peptide bound to Ctf4. The stapled Sld5 peptide was able to displace the Ctf4 partner DNA polymerase α from the replisome in yeast extracts. Our study provides proof-of-principle evidence for the development of small-molecule inhibitors of the human CTF4 orthologue AND-1.


  • Organizational Affiliation

    Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, 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
479Saccharomyces 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
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU
D, E
19Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03406 
Go to UniProtKB:  Q03406
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03406
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.679α = 90
b = 100.287β = 90
c = 219.749γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description