+Open data
-Basic information
Entry | Database: PDB / ID: 3bqo | ||||||
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Title | Crystal Structure of TRF1 TRFH domain and TIN2 peptide complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / TRF1 TRFH domain Dimerization domain TIN2 / ADP-ribosylation / Alternative splicing / Cell cycle / Cell division / Chromosomal protein / DNA-binding / Mitosis / Nucleus / Phosphoprotein / Telomere | ||||||
Function / homology | Function and homology information regulation of telomere maintenance via telomere lengthening / perinucleolar chromocenter / 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 / telomere assembly / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly ...regulation of telomere maintenance via telomere lengthening / perinucleolar chromocenter / 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 / telomere assembly / 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 / meiotic telomere clustering / 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 / : / positive regulation of telomere maintenance / nuclear telomere cap complex / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / telomere capping / Telomere Extension By Telomerase / DNA binding, bending / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via 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 / Meiotic synapsis / Inhibition of DNA recombination at telomere / telomere maintenance / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / nuclear matrix / spindle / negative regulation of epithelial cell proliferation / chromosome, telomeric region / microtubule binding / nuclear body / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 | 3bqo.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bqo.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bqo_validation.pdf.gz | 435.6 KB | Display | wwPDB validaton report |
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Full document | 3bqo_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 3bqo_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3bqo_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/3bqo ftp://data.pdbj.org/pub/pdb/validation_reports/bq/3bqo | HTTPS FTP |
-Related structure data
Related structure data | 3bu8C 3buaC 1h6oS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24216.666 Da / Num. of mol.: 1 / Fragment: TRFH domain, Dimerization domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Plasmid: PET 28B-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P54274 |
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#2: Protein/peptide | Mass: 2472.787 Da / Num. of mol.: 1 / Fragment: Nuclear localization signal Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TINF2, TIN2 / Plasmid: PET 28B-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 256 B CAME FROM A PROTEASE SPECIFIC DIGESTION. IT IS A RESIDUAL RESIDUE AFTER DIGESTION. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.31 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: NaCl 2.5 M MgCl2 0.35 M Tris 0.1 M pH 8.6 DTT 5 mM , VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 24553 / Num. obs: 24517 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 20.2 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 50.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 7.4 / Num. unique all: 2388 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H6O Resolution: 2→50 Å / σ(F): 0
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Displacement parameters | Biso mean: 36.3825 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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