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 1.1 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: 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, repre ...

    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.

    Related Citations: 
    • A Ctf4 trimer couples the CMG helicase to DNA polymerase alpha in the eukaryotic replisome.
      Simon, A.C., Zhou, J.C., Perera, R.L., van Deursen, F., Evrin, C., Ivanova, M.E., Kilkenny, M.L., Renault, L., Kjaer, S., Matak-Vinkovic, D., Labib, K., Costa, A., Pellegrini, L.
      (2014) Nature 510: 293
    Organizational Affiliation: 

    Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase alpha-binding protein A, B, C479Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CTF4, CHL15, POB1, YPR135W, P9659.7
Find proteins for Q01454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q01454 
Go to UniProtKB:  Q01454
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU D, E19Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03406 
Go to UniProtKB:  Q03406
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
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

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-05-10 
  • Released Date: 2017-08-30 
    • Deposition Author(s): Wu, Y., Pellegrini, L.
Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104641/Z/14/Z

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-10-11
    Changes: Database references