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 GGGGTTTTGG ...

    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 subunitA495Sterkiella novaMutation(s): 0 
Gene Names: MAC-56AMAC-56KMAC-56S
Find proteins for P29549 (Sterkiella nova)
Explore P29549 
Go to UniProtKB:  P29549
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
telomere-binding protein beta subunitB260Sterkiella 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
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CL
    Query on CL

    Download CCD File 
    B
    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: 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 

    • 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