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: 2.413 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 

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

  • 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, r ...

    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 Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase alpha-binding protein
A, B, C
479Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CTF4 (CHL15, POB1)
Find proteins for Q01454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01454
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MET-ASP-ILE-UA1-ILE-ASP-ASP-ILE-LEU-UA2-GLU-LEU-ASP-LYS-GLU
D, E
19Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SLD5
Find proteins for Q03406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03406
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
9FZ
Query on 9FZ
D, E
NON-POLYMERC8 H14 N4 O2

--

9G2
Query on 9G2
D, E
NON-POLYMERC9 H16 N4 O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.413 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 88.679α = 90.00
b = 100.287β = 90.00
c = 219.749γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references