+Open data
-Basic information
Entry | Database: PDB / ID: 3bu8 | ||||||
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Title | Crystal Structure of TRF2 TRFH domain and TIN2 peptide complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / TRF2 TRFH domain TRF2 dimerization domain TIN2 peptide / Alternative splicing / Cell cycle / Chromosomal protein / DNA-binding / Nucleus / Phosphoprotein / Telomere | ||||||
Function / homology | Function and homology information regulation of telomere maintenance via telomere lengthening / perinucleolar chromocenter / 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 / telomere assembly / negative regulation of telomere maintenance / negative regulation of telomere maintenance via semi-conservative replication ...regulation of telomere maintenance via telomere lengthening / perinucleolar chromocenter / 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 / telomere assembly / negative regulation of telomere maintenance / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of protein ADP-ribosylation / protection from non-homologous end joining at telomere / negative regulation of telomere capping / 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 / Telomere C-strand (Lagging Strand) Synthesis / regulation of telomere maintenance via telomerase / 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 / Removal of the Flap Intermediate from the C-strand / anterograde axonal transport / 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 / axon cytoplasm / 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 / male germ cell nucleus / positive regulation of nitric-oxide synthase activity / DNA Damage/Telomere Stress Induced Senescence / nuclear matrix / negative regulation of epithelial cell proliferation / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / cell cycle / negative regulation of gene expression / protein-containing complex binding / positive regulation of gene expression / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Chen, Y. / Yang, Y. / van Overbeek, M. / Donigian, J.R. / Baciu, P. / de Lange, T. / Lei, M. | ||||||
Citation | Journal: Science / Year: 2008 Title: A shared docking motif in TRF1 and TRF2 used for differential recruitment of telomeric proteins. Authors: Chen, Y. / Yang, Y. / van Overbeek, M. / Donigian, J.R. / Baciu, P. / de Lange, T. / Lei, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bu8.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bu8.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3bu8 ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3bu8 | HTTPS FTP |
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-Related structure data
Related structure data | 3bqoC 3buaC 1h6pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26957.195 Da / Num. of mol.: 2 / Fragment: TRFH domain, Dimerization domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Plasmid: PET28B-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q15554 #2: Protein/peptide | Mass: 2177.446 Da / Num. of mol.: 2 / Fragment: UNP residues 2-19 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TINF2, TIN2 / Plasmid: PET28b-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9BSI4 #3: Water | ChemComp-HOH / | Sequence details | THE RESIDUE SER 257 C AND SER 257 D CAME FROM A PROTEASE SPECIFIC DIGESTION. IT IS A RESIDUAL ...THE RESIDUE SER 257 C AND SER 257 D CAME FROM A PROTEASE SPECIFIC DIGESTION. IT IS A RESIDUAL RESIDUE AFTER DIGESTION. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.22 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG550 MME 14%, HEPES.Na 50 mM Tris.HCl 40 mM, MgCl2 5 mM, DTT 2 mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
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Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→500 Å / Num. all: 28812 / Num. obs: 28753 / % possible obs: 99.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 47.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 41.78 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 5.63 / Num. unique all: 2828 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H6P Resolution: 2.15→500 Å / σ(F): 0
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Displacement parameters | Biso mean: 51.83 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→500 Å
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Refine LS restraints |
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