1JB7

DNA G-Quartets in a 1.86 A Resolution Structure of an Oxytricha nova Telomeric Protein-DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex.

Horvath, M.P.Schultz, S.C.

(2001) J Mol Biol 310: 367-377

  • DOI: 10.1006/jmbi.2001.4766
  • Primary Citation of Related Structures:  
    1JB7

  • PubMed Abstract: 
  • The Oxytricha nova telomere end binding protein (OnTEBP) recognizes, binds and protects the single-stranded 3'-terminal DNA extension found at the ends of macronuclear chromosomes. The structure of this complex shows that the single strand GGGGTTTTGGGG DNA binds in a deep cleft between the two protein subunits of OnTEBP, adopting a non-helical and irregular conformation ...

    The Oxytricha nova telomere end binding protein (OnTEBP) recognizes, binds and protects the single-stranded 3'-terminal DNA extension found at the ends of macronuclear chromosomes. The structure of this complex shows that the single strand GGGGTTTTGGGG DNA binds in a deep cleft between the two protein subunits of OnTEBP, adopting a non-helical and irregular conformation. In extending the resolution limit of this structure to 1.86 A, we were surprised to find a G-quartet linked dimer of the GGGGTTTTGGGG DNA also packing within the crystal lattice and interacting with the telomere end binding protein. The G-quartet DNA exhibits the same structure and topology as previously observed in solution by NMR with diagonally crossing d(TTTT) loops at either end of the four-stranded helix. Additionally, the crystal structure reveals clearly visible Na(+), and specific patterns of bound water molecules in the four non-equivalent grooves. Although the G-quartet:protein contact surfaces are modest and might simply represent crystal packing interactions, it is interesting to speculate that the two types of telomeric DNA-protein interactions observed here might both be important in telomere biology.


    Related Citations: 
    • Crystal Structure of the Oxytricha Nova Telomere End Binding Protein Complexed with Single Strand DNA
      Horvath, M.P., Schweiker, V.L., Bevilacqua, J.M., Ruggles, J.A., Schultz, S.C.
      (1998) Cell 95: 963
    • Refined Solution Structure of the Dimeric Quadruplex Formed from the Oxytricha Telomeric Oligonucleotide d(GGGGTTTTGGGG)
      Schultze, P., Smith, F.W., Feigon, J.
      (1994) Structure 2: 221

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA. Horvath@biology.utah.edu



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
telomere-binding protein alpha subunit A495Sterkiella novaMutation(s): 0 
Gene Names: MAC-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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
telomere-binding protein beta subunit B260Sterkiella novaMutation(s): 0 
Gene Names: MAC-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*G)-3'D, G, H12N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.86 Å
    • R-Value Free: 0.246 
    • R-Value Work: 0.230 
    • R-Value Observed: 0.232 
    • Space Group: P 61 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 93.1α = 90
    b = 93.1β = 90
    c = 421.8γ = 120
    Software Package:
    Software NamePurpose
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2001-06-11
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance
    • Version 1.3: 2011-11-16
      Changes: Atomic model