5NW5

Crystal structure of the Rif1 N-terminal domain (RIF1-NTD) from Saccharomyces cerevisiae in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.502 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends.

Mattarocci, S.Reinert, J.K.Bunker, R.D.Fontana, G.A.Shi, T.Klein, D.Cavadini, S.Faty, M.Shyian, M.Hafner, L.Shore, D.Thoma, N.H.Rass, U.

(2017) Nat. Struct. Mol. Biol. 24: 588-595

  • DOI: 10.1038/nsmb.3420
  • Primary Citation of Related Structures:  5NVR

  • PubMed Abstract: 
  • In yeast, Rif1 is part of the telosome, where it inhibits telomerase and checkpoint signaling at chromosome ends. In mammalian cells, Rif1 is not telomeric, but it suppresses DNA end resection at chromosomal breaks, promoting repair by nonhomologous ...

    In yeast, Rif1 is part of the telosome, where it inhibits telomerase and checkpoint signaling at chromosome ends. In mammalian cells, Rif1 is not telomeric, but it suppresses DNA end resection at chromosomal breaks, promoting repair by nonhomologous end joining (NHEJ). Here, we describe crystal structures for the uncharacterized and conserved ∼125-kDa N-terminal domain of Rif1 from Saccharomyces cerevisiae (Rif1-NTD), revealing an α-helical fold shaped like a shepherd's crook. We identify a high-affinity DNA-binding site in the Rif1-NTD that fully encases DNA as a head-to-tail dimer. Engagement of the Rif1-NTD with telomeres proved essential for checkpoint control and telomere length regulation. Unexpectedly, Rif1-NTD also promoted NHEJ at DNA breaks in yeast, revealing a conserved role of Rif1 in DNA repair. We propose that tight associations between the Rif1-NTD and DNA gate access of processing factors to DNA ends, enabling Rif1 to mediate diverse telomere maintenance and DNA repair functions.


    Organizational Affiliation

    Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Telomere length regulator protein RIF1
A, B
1226Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RIF1
Find proteins for P29539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RIF1
Go to UniProtKB:  P29539
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (60-MER)C30synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (30-MER)D30synthetic construct
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 92.140α = 90.00
b = 169.800β = 90.00
c = 390.160γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Type: Database references
  • Version 1.2: 2017-07-19
    Type: Database references