Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 9594.80 
• Atom Count: 678 
• Residue Count: 83 
• Unique protein chains: 1

2CKX

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

• DOI: 10.2210/pdb2CKX/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Nicotiana tabacum
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-04-24 Released: 2007-05-29 
• Deposition Author(s): Byun, J.-S., Cho, H.-S.

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Experimental Data Snapshot

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

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

• PubMed: 18367475 
• 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 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).

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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
Molecule	Chains	Sequence Length	Organism	Details
TELOMERE BINDING PROTEIN TBP1	A	83	Nicotiana tabacum	Mutation(s): 0  Gene 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 = 40.122	α = 90.00
b = 48.265	β = 90.00
c = 52.006	γ = 90.00

Software Package:

Software Name	Purpose
SHELX	phasing
CNS	refinement
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-24 
• Released Date: 2007-05-29 
• Deposition Author(s): Byun, J.-S., Cho, H.-S.

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