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- PDB-1w0u: hTRF2 DNA-binding domain in complex with telomeric DNA. -

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Basic information

Entry
Database: PDB / ID: 1w0u
TitlehTRF2 DNA-binding domain in complex with telomeric DNA.
Components
  • 5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP *CP*CP*CP*TP*AP*GP*A)-3'
  • 5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP *GP*GP*GP*TP*TP*AP*G)-3'
  • TELOMERIC REPEAT BINDING FACTOR 2
KeywordsDNA BINDING PROTEIN / TELOMERE / DNA-BINDING PROTEIN / HOMEODOMAIN / MITOSIS / CELL CYCLE / NUCLEAR PROTEIN / CHROMOSOMAL PROTEIN / PHOSPHORYLATION / ADP-RIBOSYLATION
Function / homology
Function and homology information


axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere ...axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / negative regulation of t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / anterograde axonal transport / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / regulation of telomere maintenance / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / axon cytoplasm / 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 / positive regulation of nitric-oxide synthase activity / male germ cell nucleus / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / negative regulation of gene expression / positive regulation of gene expression / protein-containing complex binding / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus
Similarity search - Function
Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / 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 ...Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / 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 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 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
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TELOMERIC REPEAT BINDING FACTOR 2
B: TELOMERIC REPEAT BINDING FACTOR 2
C: 5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP *GP*GP*GP*TP*TP*AP*G)-3'
D: 5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP *CP*CP*CP*TP*AP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)23,5314
Polymers23,5314
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.080, 46.780, 107.460
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 2 / TTAGGG REPEAT-BINDING FACTOR 2 / TELOMERIC DNA BINDING PROTEIN


Mass: 6558.615 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 446-500
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SYNTHETIC GENE / Plasmid: PET30A/TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q15554
#2: DNA chain 5'-D(*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP *GP*GP*GP*TP*TP*AP*G)-3'


Mass: 5313.442 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP *CP*CP*CP*TP*AP*GP*A)-3'


Mass: 5100.340 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 45.71 %
Crystal growpH: 6
Details: CRYSTALS WERE GROWN FROM 50 MM MES, PH 6.0, 5MM MAGNESIUM ACETATE, 1 MM SPERMINE, AND 2M (NH4)2SO4 AND CRYOPROTECTED IN 15 % 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: 1.8→34.08 Å / Num. obs: 21000 / % possible obs: 98.7 % / Redundancy: 8 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 8.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
autoSHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MIR / Resolution: 1.8→34.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1317285.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2074 9.9 %RANDOM
Rwork0.22 ---
obs0.22 21000 98.4 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.390634 e/Å3
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.27 Å20 Å20 Å2
2--5.17 Å20 Å2
3----2.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å-
Refinement stepCycle: LAST / Resolution: 1.8→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 671 0 130 1723
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 336 9.9 %
Rwork0.198 3060 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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