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)  |  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
Protein Feature View
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  • Reference Sequence
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  • 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
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   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
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      • 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




      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