PDBsum entry 1ba5

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protein links
DNA-binding domain PDB id
Protein chain
53 a.a. *
* Residue conservation analysis
PDB id:
Name: DNA-binding domain
Title: DNA-binding domain of human telomeric protein, htrf1, nmr, 18 structures
Structure: Htrf1. Chain: a. Fragment: DNA-binding domain. Synonym: telomeric repeat binding factor 1. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cellular_location: nucleus
NMR struc: 18 models
Authors: T.Nishikawa,A.Nagadoi,S.Yoshimura,S.Aimoto,Y.Nishimura
Key ref:
T.Nishikawa et al. (1998). Solution structure of the DNA-binding domain of human telomeric protein, hTRF1. Structure, 6, 1057-1065. PubMed id: 9739097 DOI: 10.1016/S0969-2126(98)00106-3
22-Apr-98     Release date:   27-Apr-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P54274  (TERF1_HUMAN) -  Telomeric repeat-binding factor 1
439 a.a.
53 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     chromatin binding     2 terms  


DOI no: 10.1016/S0969-2126(98)00106-3 Structure 6:1057-1065 (1998)
PubMed id: 9739097  
Solution structure of the DNA-binding domain of human telomeric protein, hTRF1.
T.Nishikawa, A.Nagadoi, S.Yoshimura, S.Aimoto, Y.Nishimura.
BACKGROUND: Mammalian telomeres consist of long tandem arrays of the double-stranded TTAGGG sequence motif packaged by a telomere repeat binding factor, TRF1. The DNA-binding domain of TRF1 shows sequence homology to each of three tandem repeats of the DNA-binding domain of the transcriptional activator c-Myb. The isolated c-Myb-like domain of human TRF1 (hTRF1) binds specifically to telomeric DNA as a monomer, in a similar manner to that of homeodomains. So far, the only three-dimensional structure of a telomeric protein to be determined is that of a yeast telomeric protein, Rap 1p. The DNA-binding domain of Rap 1p contains two subdomains that are structurally closely related to c-Myb repeats. We set out to determine the solution structure of the DNA-binding domain of hTRF1 in order to establish its mode of DNA binding. RESULTS: The solution structure of the DNA-binding domain of hTRF1 has been determined and shown to comprise three helices. The architecture of the three helices is very similar to that of each Rap 1p subdomain and also to that of each c-Myb repeat. The second and third helix form a helix-turn-helix (HTH) variant. The length of the third helix of hTRF1 is similar to that of the second subdomain of Rap 1p. CONCLUSIONS: The hTRF1 DNA-binding domain is likely to bind to DNA in a similar manner to that of the second subdomain of Rap 1p. On the basis of the Rap 1p-DNA complex, a model of the hTRF1 DNA-binding domain in complex with human telomeric DNA was constructed. In addition to DNA recognition by the HTH variant, a flexible N-terminal arm of hTRF1 is likely to interact with DNA.
  Selected figure(s)  
Figure 3.
Figure 3. Stereoviews of the hTRF1 DNA-binding domain structures. Backbone atoms and sidechain atoms are shown in yellow and red, respectively; the N and C termini are marked. (a) The best-fit superposition of the 18 structures; three tryptophans and one phenylalanine residue form the hydrophobic core. (b) The refined average structure again showing the amino acids that form the hydrophobic core.
  The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1057-1065) copyright 1998.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20191372 I.Ourliac-Garnier, A.Poulet, R.Charif, S.Amiard, F.Magdinier, K.Rezaï, E.Gilson, M.J.Giraud-Panis, and S.Bombard (2010).
Platination of telomeric DNA by cisplatin disrupts recognition by TRF2 and TRF1.
  J Biol Inorg Chem, 15, 641-654.  
19887064 K.Tahmaseb, and J.J.Turchi (2010).
Intrinsic hTRF1 fluorescence quenching reveals details of telomere DNA binding activity: impact of DNA length, structure and position of telomeric repeats.
  Arch Biochem Biophys, 493, 207-212.  
19445951 B.G.Wensley, M.Gärtner, W.X.Choo, S.Batey, and J.Clarke (2009).
Different members of a simple three-helix bundle protein family have very different folding rate constants and fold by different mechanisms.
  J Mol Biol, 390, 1074-1085.  
19724792 I.J.Lee, J.W.Yi, and B.H.Kim (2009).
Probe for i-motif structure and G-rich strands using end-stacking ability.
  Chem Commun (Camb), (), 5383-5385.  
19132417 P.Cysewski, and P.Czeleń (2009).
Structural and energetic heterogeneities of canonical and oxidized central guanine triad of B-DNA telomeric fragments.
  J Mol Model, 15, 607-613.  
18367475 S.Ko, S.H.Jun, H.Bae, J.S.Byun, W.Han, H.Park, S.W.Yang, S.Y.Park, Y.H.Jeon, C.Cheong, W.T.Kim, W.Lee, and H.S.Cho (2008).
Structure of the DNA-binding domain of NgTRF1 reveals unique features of plant telomere-binding proteins.
  Nucleic Acids Res, 36, 2739-2755.
PDB code: 2ckx
15688221 M.G.Hwang, K.Kim, W.K.Lee, and M.H.Cho (2005).
AtTBP2 and AtTRP2 in Arabidopsis encode proteins that bind plant telomeric DNA and induce DNA bending in vitro.
  Mol Genet Genomics, 273, 66-75.  
15608617 R.Court, L.Chapman, L.Fairall, and D.Rhodes (2005).
How the human telomeric proteins TRF1 and TRF2 recognize telomeric DNA: a view from high-resolution crystal structures.
  EMBO Rep, 6, 39-45.
PDB codes: 1w0t 1w0u
15364931 Z.N.Karamysheva, Y.V.Surovtseva, L.Vespa, E.V.Shakirov, and D.E.Shippen (2004).
A C-terminal Myb extension domain defines a novel family of double-strand telomeric DNA-binding proteins in Arabidopsis.
  J Biol Chem, 279, 47799-47807.  
14987434 A.P.Voronin, I.B.Lobov, E.Gilson, and O.I.Podgornaya (2003).
A telomere-binding protein (TRF2/MTBP) from mouse nuclear matrix with motives of an intermediate filament-type rod domain.
  J Anti Aging Med, 6, 205-218.  
12475927 D.Rhodes, L.Fairall, T.Simonsson, R.Court, and L.Chapman (2002).
Telomere architecture.
  EMBO Rep, 3, 1139-1145.  
12354778 L.Mohrmann, A.J.Kal, and C.P.Verrijzer (2002).
Characterization of the extended Myb-like DNA-binding domain of trithorax group protein Zeste.
  J Biol Chem, 277, 47385-47392.  
11545737 L.Fairall, L.Chapman, H.Moss, Lange, and D.Rhodes (2001).
Structure of the TRFH dimerization domain of the human telomeric proteins TRF1 and TRF2.
  Mol Cell, 8, 351-361.
PDB codes: 1h6o 1h6p
11591318 M.Nakamura, X.Z.Zhou, S.Kishi, I.Kosugi, Y.Tsutsui, and K.P.Lu (2001).
A specific interaction between the telomeric protein Pin2/TRF1 and the mitotic spindle.
  Curr Biol, 11, 1512-1516.  
11738049 T.Nishikawa, H.Okamura, A.Nagadoi, P.König, D.Rhodes, and Y.Nishimura (2001).
Solution structure of a telomeric DNA complex of human TRF1.
  Structure, 9, 1237-1251.
PDB codes: 1ity 1iv6
10523316 A.Bianchi, R.M.Stansel, L.Fairall, J.D.Griffith, D.Rhodes, and Lange (1999).
TRF1 binds a bipartite telomeric site with extreme spatial flexibility.
  EMBO J, 18, 5735-5744.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.