1PH8

CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGCGG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes

Theobald, D.L.Schultz, S.C.

(2003) EMBO J 22: 4314-4324

  • DOI: 10.1093/emboj/cdg415
  • Primary Citation of Related Structures:  
    1PA6, 1PH9, 1PH8, 1PH7, 1PH6, 1PH5, 1PH4, 1PH3, 1PH2, 1PH1

  • PubMed Abstract: 
  • Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore ...

    Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA. theobal@colorado.edu



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Telomere-binding protein alpha subunitA460Sterkiella novaMutation(s): 0 
Gene Names: MAC-56A AND MAC-56K AND MAC-56SMAC-56AMAC-56KMAC-56S
Find proteins for P29549 (Sterkiella nova)
Explore P29549 
Go to UniProtKB:  P29549
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Telomere-binding protein beta subunitB216Sterkiella novaMutation(s): 0 
Gene Names: MAC-41A AND MAC-41SMAC-41AMAC-41S
Find proteins for P16458 (Sterkiella nova)
Explore P16458 
Go to UniProtKB:  P16458
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*T)-3'G, H13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*CP*GP*G)-3'D12N/A
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CL
      Query on CL

      Download CCD File 
      A
      CHLORIDE ION
      Cl
      VEXZGXHMUGYJMC-UHFFFAOYSA-M
       Ligand Interaction
      NA
      Query on NA

      Download CCD File 
      G, H
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.36 Å
      • R-Value Free: 0.256 
      • R-Value Work: 0.222 
      • R-Value Observed: 0.222 
      • Space Group: P 61 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 93.472α = 90
      b = 93.472β = 90
      c = 423.554γ = 120
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2003-06-17
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance