1IGN

DNA-BINDING DOMAIN OF RAP1 IN COMPLEX WITH TELOMERIC DNA SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA.

Konig, P.Giraldo, R.Chapman, L.Rhodes, D.

(1996) Cell 85: 125-136


  • PubMed Abstract: 
  • Telomeres, the nucleoprotein complexes at the ends of eukaryotic chromosomes, are essential for chromosome stability. In the yeast S. cerevisiae, telomeric DNA is bound in a sequence-specific manner by RAP1, a multifunctional protein also involved in ...

    Telomeres, the nucleoprotein complexes at the ends of eukaryotic chromosomes, are essential for chromosome stability. In the yeast S. cerevisiae, telomeric DNA is bound in a sequence-specific manner by RAP1, a multifunctional protein also involved in transcriptional regulation. Here we report the crystal structure of the DNA-binding domain of RAP1 in complex with telomeric DNA site at 2.25 A resolution. The protein contains two similar domains that bind DNA in a tandem orientation, recognizing a tandemly repeated DNA sequence. The domains are structurally related to the homeodomain and the proto-oncogene Myb, but show novel features in their DNA-binding mode. A structured linker between the domains and a long C-terminal tail contribute to the binding specificity. This structure provides insight into the recognition of the conserved telomeric DNA sequences by a protein.


    Related Citations: 
    • Purification and Cloning of a DNA Binding Protein from Yeast that Binds to Both Silencer and Activator Elements
      Shore, D.,Nasmyth, K.
      (1987) Cell 51: 721
    • The Yeast Telomere-Binding Protein RAP1 Binds to and Promotes the Formation of DNA Quadruplexes in Telomeric DNA
      Giraldo, R.,Rhodes, D.
      (1994) Embo J. 13: 2411


    Organizational Affiliation

    Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (RAP1)
A, B
246Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: RAP1 (GRF1, TUF1)
Find proteins for P11938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P11938
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')C,E19N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')D,F19N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.219 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 90.610α = 90.00
b = 90.610β = 90.00
c = 80.360γ = 120.00
Software Package:
Software NamePurpose
CCP4data reduction
X-PLORrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-01-27
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Database references