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- PDB-1w0t: hTRF1 DNA-binding domain in complex with telomeric DNA. -

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Basic information

Entry
Database: PDB / ID: 1w0t
TitlehTRF1 DNA-binding domain in complex with telomeric DNA.
Components
  • 5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP *TP*AP*GP*GP*GP*TP*TP*AP*G)-3'
  • 5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP *AP*CP*CP*CP*TP*AP*AP*CP*A)-3'
  • TELOMERIC REPEAT BINDING FACTOR 1
KeywordsDNA BINDING PROTEIN / TELOMERE / DNA-BINDING PROTEIN / HOMEODOMAIN / MITOSIS / CELL CYCLE / NUCLEAR PROTEIN / CHROMOSOMAL PROTEIN / PHOSPHORYLATION / ADP-RIBOSYLATION
Function / homology
Function and homology information


positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomeric D-loop disassembly / t-circle formation ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomeric D-loop disassembly / t-circle formation / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the C-strand of the telomere / nuclear telomere cap complex / G-rich strand telomeric DNA binding / positive regulation of telomere maintenance / Polymerase switching on the C-strand of the telomere / ankyrin repeat binding / Removal of the Flap Intermediate from the C-strand / telomere capping / negative regulation of telomere maintenance via telomerase / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomerase activity / Telomere Extension By Telomerase / telomere maintenance via telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / spindle / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / microtubule binding / chromosome, telomeric region / molecular adaptor activity / nuclear body / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like ...Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Telomeric repeat-binding factor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsCourt, R.I. / Chapman, L.M. / Fairall, L. / Rhodes, D.
CitationJournal: Embo Rep. / Year: 2005
Title: How the Human Telomeric Proteins Trf1 and Trf2 Recognize Telomeric DNA: A View from High-Resolution Crystal Structures
Authors: Court, R.I. / Chapman, L.M. / Fairall, L. / Rhodes, D.
History
DepositionJun 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TELOMERIC REPEAT BINDING FACTOR 1
B: TELOMERIC REPEAT BINDING FACTOR 1
C: 5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP *TP*AP*GP*GP*GP*TP*TP*AP*G)-3'
D: 5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP *AP*CP*CP*CP*TP*AP*AP*CP*A)-3'


Theoretical massNumber of molelcules
Total (without water)24,9064
Polymers24,9064
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.443, 72.360, 116.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TELOMERIC REPEAT BINDING FACTOR 1 / TTAGGG REPEAT-BINDING FACTOR 1 / NIMA- INTERACTING PROTEIN 2 / TELOMERIC PROTEIN PIN2/TRF1


Mass: 6640.792 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 379-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PET13A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P54274
#2: DNA chain 5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP *TP*AP*GP*GP*GP*TP*TP*AP*G)-3'


Mass: 5946.842 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP *AP*CP*CP*CP*TP*AP*AP*CP*A)-3'


Mass: 5677.716 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBINDS THE TELOMERIC DOUBLE-STRANDED TTAGGG REPEAT AND NEGATIVELY REGULATES TELOMERE LENGTH.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.34 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLISED IN 50 MM MES, PH 6.0, 0.1 M KCL, 2 MM MGCL2 AND 10 % PEG 400 AND CRYOPROTECTED IN 20 % GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→23.62 Å / Num. obs: 22407 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
autoSHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2→23.62 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1187150.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2226 9.9 %RANDOM
Rwork0.252 ---
obs0.252 22407 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.3951 Å2 / ksol: 0.384795 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1-13.67 Å20 Å20 Å2
2---4.76 Å20 Å2
3----8.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→23.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 771 0 72 1759
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.41.5
X-RAY DIFFRACTIONc_mcangle_it6.732
X-RAY DIFFRACTIONc_scbond_it2.682
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 364 9.8 %
Rwork0.262 3355 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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