2CKX

Crystal structure of NgTRF1, double-stranded telomeric repeat binding factor from Nicotiana tabacum.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the DNA-Binding Domain of Ngtrf1 Reveals Unique Features of Plant Telomere-Binding Proteins.

Ko, S.Jun, S.Bae, H.Byun, J.-S.Han, W.Park, H.Yang, S.W.Park, S.Jeon, Y.H.Cheong, C.Kim, W.T.Lee, W.Cho, H.-S.

(2008) Nucleic Acids Res. 36: 2739

  • DOI: 10.1093/nar/gkn030

  • PubMed Abstract: 
  • Telomeres are protein-DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domai ...

    Telomeres are protein-DNA elements that are located at the ends of linear eukaryotic chromosomes. In concert with various telomere-binding proteins, they play an essential role in genome stability. We determined the structure of the DNA-binding domain of NgTRF1, a double-stranded telomere-binding protein of tobacco, using multidimensional NMR spectroscopy and X-ray crystallography. The DNA-binding domain of NgTRF1 contained the Myb-like domain and C-terminal Myb-extension that is characteristic of plant double-stranded telomere-binding proteins. It encompassed amino acids 561-681 (NgTRF1(561-681)), and was composed of 4 alpha-helices. We also determined the structure of NgTRF1(561-681) bound to plant telomeric DNA. We identified several amino acid residues that interacted directly with DNA, and confirmed their role in the binding of NgTRF1 to telomere using site-directed mutagenesis. Based on a structural comparison of the DNA-binding domains of NgTRF1 and human TRF1 (hTRF1), NgTRF1 has both common and unique DNA-binding properties. Interaction of Myb-like domain with telomeric sequences is almost identical in NgTRF1(561-681) with the DNA-binding domain of hTRF1. The interaction of Arg-638 with the telomeric DNA, which is unique in NgTRF1(561-681), may provide the structural explanation for the specificity of NgTRF1 to the plant telomere sequences, (TTTAGGG)(n).


    Organizational Affiliation

    Department of Biochemistry, Department of Biology, Protein Network Research Center, College of Life Sciences and Biotechnology, Yonsei University, Seoul 120-749, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TELOMERE BINDING PROTEIN TBP1
A
83Nicotiana tabacumGene Names: NtTBP1
Find proteins for A0ZPR8 (Nicotiana tabacum)
Go to UniProtKB:  A0ZPR8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.122α = 90.00
b = 48.265β = 90.00
c = 52.006γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2011-06-02
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance