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 

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

  • 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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
telomere-binding protein alpha subunit
A
495Sterkiella novaGene Names: MAC-56A, MAC-56K, MAC-56S
Find proteins for P29549 (Sterkiella nova)
Go to UniProtKB:  P29549
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
telomere-binding protein beta subunit
B
260Sterkiella novaGene Names: MAC-41A, MAC-41S
Find proteins for P16458 (Sterkiella nova)
Go to UniProtKB:  P16458
Entity ID: 1
MoleculeChainsLengthOrganism
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
NA
Query on NA

Download SDF File 
Download CCD File 
G, H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 93.100α = 90.00
b = 93.100β = 90.00
c = 421.800γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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