4BJ1 | pdb_00004bj1

Crystal structure of Saccharomyces cerevisiae RIF2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 
    0.229 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4BJ1

This is version 1.1 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: https://doi.org/10.1016/j.cell.2013.05.007
  • Primary Citation Related Structures: 
    4BJ1, 4BJ5, 4BJ6, 4BJS, 4BJT

  • 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. 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.

Macromolecule Content 

  • Total Structure Weight: 36.84 kDa 
  • Atom Count: 2,088 
  • Modeled Residue Count: 261 
  • Deposited Residue Count: 319 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN RIF2319Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for Q06208 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06208 
Go to UniProtKB:  Q06208
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06208
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free:  0.229 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.36α = 90
b = 78.36β = 90
c = 236.21γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing

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: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other