5NW5

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

Summary for 5NW5

• Entry DOI: 10.2210/pdb5nw5/pdb
• Related: 5NVR
• Descriptor: Telomere length regulator protein RIF1, DNA (60-MER), DNA (30-MER) (3 entities in total)
• Functional Keywords: telomere maintenance, dna double-strand break repair, irregular helical repeat, all-alpha fold, dna binding protein
• Biological source: Saccharomyces cerevisiae S288c (Baker's yeast); More
• Total number of polymer chains: 4
• Total formula weight: 299995.20

Authors

Bunker, R.D.,Reinert, J.K.,Shi, T.,Thoma, N.H. (deposition date: 2017-05-05, release date: 2017-06-14, Last modification date: 2024-01-17)

Primary citation

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.
Rif1 maintains telomeres and mediates DNA repair by encasing DNA ends.
Nat. Struct. Mol. Biol., 24:588-595, 2017

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.

PubMed: 28604726
DOI: 10.1038/nsmb.3420

Experimental method

X-RAY DIFFRACTION (6.502 Å)