+Open data
-Basic information
Entry | Database: PDB / ID: 1h6o | ||||||
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Title | Dimerisation domain from human TRF1 | ||||||
Components | TELOMERIC REPEAT BINDING FACTOR 1 | ||||||
Keywords | TELOMERE BINDING / TRF1 / TELOMERE / DIMERISATION / TRFH / DNA-BINDING / NUCLEAR PROTEIN | ||||||
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 / DNA Damage/Telomere Stress Induced Senescence / spindle / 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 | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.9 Å | ||||||
Authors | Fairall, L. / Chapman, L. / Rhodes, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Structure of the TRFH dimerization domain of the human telomeric proteins TRF1 and TRF2. Authors: Fairall, L. / Chapman, L. / Moss, H. / de Lange, T. / Rhodes, D. #1: Journal: Science / Year: 1995 Title: A Human Telomeric Protein Authors: Chong, L. / Van Steensel, B. / Broccoli, D. / Erdjument-Bromage, H. / Hannish, J. / Tempst, P. / de Lange, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h6o.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h6o.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6o ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6o | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23326.758 Da / Num. of mol.: 1 / Fragment: DIMERISATION DOMAIN RESIDUES 63-265 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: NUCLEUSCell nucleus / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54274 |
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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: 3.2 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PH6, 5-15% GLYCEROL, 1-5 MM MAGNESIUM ACETATE, 1 % PEG 8000, pH 6.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→23.69 Å / Num. obs: 8514 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 60.65 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5 / Rsym value: 0.14 / % possible all: 97.1 |
Reflection | *PLUS Num. measured all: 45019 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.9→24.84 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 4200344.17 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / ksol: 0.290203 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→24.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.25 / Rfactor Rwork: 0.25 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.4 |