1W0T | pdb_00001w0t

hTRF1 DNA-binding domain in complex with telomeric DNA.

• PDB DOI: https://doi.org/10.2210/pdb1W0T/pdb
• NAKB: 1W0T

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-06-11 Released: 2004-12-22 
• Deposition Author(s): Court, R.I., Chapman, L.M., Fairall, L., Rhodes, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.252 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Literature

How the Human Telomeric Proteins Trf1 and Trf2 Recognize Telomeric DNA: A View from High-Resolution Crystal Structures

Court, R.I., Chapman, L.M., Fairall, L., Rhodes, D.

(2005) EMBO Rep 6: 39

• PubMed: 15608617 
• DOI: https://doi.org/10.1038/sj.embor.7400314
• Primary Citation Related Structures: 
  1W0T, 1W0U


• PubMed Abstract: 
  

  Human telomeres consist of tandem arrays of TTAGGG sequence repeats that are specifically bound by two proteins, TRF1 and TRF2. They bind to DNA as preformed homodimers and have the same architecture in which the DNA-binding domains (Dbds) form independent structural units. Despite these similarities, TRF1 and TRF2 have different functions at telomeres. The X-ray crystal structures of both TRF1- and TRF2-Dbds in complex with telomeric DNA (2.0 and 1.8 angstroms resolution, respectively) show that they recognize the same TAGGGTT binding site by means of homeodomains, as does the yeast telomeric protein Rap1p. Two of the three G-C base pairs that characterize telomeric repeats are recognized specifically and an unusually large number of water molecules mediate protein-DNA interactions. The binding of the TRF2-Dbd to the DNA double helix shows no distortions that would account for the promotion of t-loops in which TRF2 has been implicated.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.91 kDa 
• Atom Count: 1,759 
• Modeled Residue Count: 142 
• Deposited Residue Count: 144 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TELOMERIC REPEAT BINDING FACTOR 1	A, B	53	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P54274 (Homo sapiens) Explore P54274  Go to UniProtKB:  P54274
PHAROS:  P54274 GTEx:  ENSG00000147601

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP *TP*AP*GP*GP*GP*TP*TP*AP*G)-3'	C	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP *AP*CP*CP*CP*TP*AP*AP*CP*A)-3'	D	19	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.252 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.443	α = 90
b = 72.36	β = 90
c = 116.706	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
autoSHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-22 
Deposition Author(s): Court, R.I., Chapman, L.M., Fairall, L., Rhodes, D.

Revision History  

• Version 1.0: 2004-12-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Other