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 
  • R-Value Observed: 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

  • DOI: 10.1016/s0092-8674(00)81088-0
  • Primary Citation of Related Structures:  
    1IGN

  • 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 transcriptional regulation ...

    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: 
    • 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
    • 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
    Organizational Affiliation: 

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



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (RAP1)E [auth A],
F [auth B]		246Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RAP1 DNA BINDING DOMAIN
UniProt
Find proteins for P11938 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11938 
Go to UniProtKB:  P11938
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11938
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*GP*CP*AP*CP*AP*CP*CP*CP*AP*CP*AP*CP*AP*CP*C P*AP*G)-3')A [auth C],
C [auth E]		19N/A
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*CP*TP*GP*GP*TP*GP*TP*GP*TP*GP*GP*GP*TP*GP*TP*G P*CP*G)-3')B [auth D],
D [auth F]		19N/A
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DNA PDBBind:  1IGN Kd: 0.01 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.61α = 90
b = 90.61β = 90
c = 80.36γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
CCP4data reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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