4BJT

Crystal structure of the Rap1 C-terminal domain (Rap1-RCT) in complex with the Rap1 binding module of Rif1 (Rif1-RBM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Rif1 and Rif2 Shape Telomere Funcation and Architecture Through Multivalent RAP1 Interactions

Shi, T.Bunker, R.D.Mattarocci, S.Ribeyre, C.Faty, M.Gut, H.Scrima, A.Rass, U.Rubin, S.M.Shore, D.Thoma, N.H.

(2013) Cell 153: 1340

  • DOI: 10.1016/j.cell.2013.05.007
  • Primary Citation of Related Structures:  
    4BJ5, 4BJ6, 4BJ1, 4BJT, 4BJS

  • PubMed Abstract: 
  • Yeast telomeres comprise irregular TG₁₋₃ DNA repeats bound by the general transcription factor Rap1. Rif1 and Rif2, along with Rap1, form the telosome, a protective cap that inhibits telomerase, counteracts SIR-mediated transcriptional silencing, and prevents inadvertent recognition of telomeres as DNA double-strand breaks ...

    Yeast telomeres comprise irregular TG₁₋₃ DNA repeats bound by the general transcription factor Rap1. Rif1 and Rif2, along with Rap1, form the telosome, a protective cap that inhibits telomerase, counteracts SIR-mediated transcriptional silencing, and prevents inadvertent recognition of telomeres as DNA double-strand breaks. We provide a molecular, biochemical, and functional dissection of the protein backbone at the core of the yeast telosome. The X-ray structures of Rif1 and Rif2 bound to the Rap1 C-terminal domain and that of the Rif1 C terminus are presented. Both Rif1 and Rif2 have separable and independent Rap1-binding epitopes, allowing Rap1 binding over large distances (42-110 Å). We identify tetramerization (Rif1) and polymerization (Rif2) modules that, in conjunction with the long-range binding, give rise to a higher-order architecture that interlinks Rap1 units. This molecular Velcro relies on Rif1 and Rif2 to recruit and stabilize Rap1 on telomeric arrays and is required for telomere homeostasis in vivo.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-BINDING PROTEIN RAP1A, B, C202Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RAP1GRF1TUF1YNL216WN1310
Find proteins for P11938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11938 
Go to UniProtKB:  P11938
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TELOMERE LENGTH REGULATOR PROTEIN RIF1D, E, F20Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RIF1YBR275CYBR1743
Find proteins for P29539 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29539 
Go to UniProtKB:  P29539
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A], H [auth B], I [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.01α = 90
b = 88.9β = 90.09
c = 57.58γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Atomic model, Other
  • Version 1.2: 2019-03-27
    Changes: Data collection, Other, Source and taxonomy