+Open data
-Basic information
Entry | Database: PDB / ID: 3bua | ||||||
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Title | Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / TRF2 TRFH domain Dimerization domain APOLLO peptide / Alternative splicing / Cell cycle / Chromosomal protein / DNA-binding / Nucleus / Phosphoprotein / Telomere / DNA damage / DNA repair / Polymorphism | ||||||
Function / homology | Function and homology information telomeric 3' overhang formation / 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 ...telomeric 3' overhang formation / 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 / telomere maintenance via telomere lengthening / 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 / Telomere Extension By Telomerase / 5'-3' exonuclease activity / regulation of telomere maintenance / protein localization to chromosome, telomeric region / 5'-3' DNA exonuclease activity / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Packaging Of Telomere Ends / male germ cell nucleus / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / interstrand cross-link repair / 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 / axon cytoplasm / telomere maintenance / DNA Damage/Telomere Stress Induced Senescence / positive regulation of nitric-oxide synthase activity / Fanconi Anemia Pathway / cellular senescence / beta-lactamase activity / double-strand break repair via nonhomologous end joining / beta-lactamase / chromosome, telomeric region / in utero embryonic development / damaged DNA binding / Hydrolases; Acting on ester bonds / nuclear body / negative regulation of gene expression / centrosome / positive regulation of gene expression / protein-containing complex binding / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 3bua.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bua.ent.gz | 147.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bua_validation.pdf.gz | 494.4 KB | Display | wwPDB validaton report |
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Full document | 3bua_full_validation.pdf.gz | 538.1 KB | Display | |
Data in XML | 3bua_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 3bua_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/3bua ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3bua | HTTPS FTP |
-Related structure data
Related structure data | 3bqoC 3bu8C 1h6pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
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Unit cell |
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-Components
#1: Protein | Mass: 23724.646 Da / Num. of mol.: 4 / Fragment: TRFH domain, dimerization domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Plasmid: PET 28B-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: 4331.907 Da / Num. of mol.: 4 / Fragment: UNP residues 495-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1B, SNM1B / Plasmid: PET 28B-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9H816 #3: Water | ChemComp-HOH / | Sequence details | THE RESIDUE SER 495 IN CHAIN E,F,G,H CAME FROM A PROTEASE SPECIFIC DIGESTION. IT IS A RESIDUAL ...THE RESIDUE SER 495 IN CHAIN E,F,G,H 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 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.53 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: (NH4)2SO4 2.6 M DTT 1 mM MES 0.05 M pH 5.6 MgAc2 10 mM, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97869 Å |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 31918 / Num. obs: 31885 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.51 / Num. unique all: 3110 / % possible all: 99.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H6P Resolution: 2.5→50 Å / σ(F): 0
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Displacement parameters | Biso mean: 40.2 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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