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: 6.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1038/nsmb.3420
  • Primary Citation of Related Structures:  
    5NVR, 5NW5

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Telomere length regulator protein RIF1
A, B
1,226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIF1YBR275CYBR1743
UniProt
Find proteins for P29539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29539 
Go to UniProtKB:  P29539
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29539
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (60-MER)30synthetic construct
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (30-MER)30synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.14α = 90
b = 169.8β = 90
c = 390.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-07-19
    Changes: Database references
  • Version 1.3: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description