+Open data
-Basic information
Entry | Database: PDB / ID: 1h6p | ||||||
---|---|---|---|---|---|---|---|
Title | Dimeristion domain from human TRF2 | ||||||
Components | TELOMERIC REPEAT BINDING FACTOR 2 | ||||||
Keywords | TELOMERE BINDING / TRF2 / TELOMERE / DIMERISATION / TRFH / DNA-BINDING / NUCLEAR PROTEIN | ||||||
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 / Telomere Extension By Telomerase / 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 / 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 / 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 / cellular senescence / chromosome, telomeric region / in utero embryonic development / 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 | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å | ||||||
Authors | Chapman, L. / Fairall, L. / Rhodes, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Structure of the Trfh Dimerization Domain of the Human Telomere Proteins Trf1 and Trf2 Authors: Fairall, L. / Chapman, L. / Moss, H. / de Lange, T. / Rhodes, D. #1: Journal: Nat.Genet. / Year: 1997 Title: Telomeric Localisation of Trf2, a Novel Human Telobox Protein Authors: Bilaud, T. / Brun, C. / Ancelin, K. / Koering, C.E. / Laroche, T. / Gilson, E. #2: Journal: Nat.Genet. / Year: 1997 Title: Human Telomere Contain Two Distinct Myb-Related Proteins, Trf1 and Trf2 Authors: Broccoli, D. / Smogorzewska, A. / Chong, L. / de Lange, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1h6p.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1h6p.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 1h6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h6p_validation.pdf.gz | 372 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1h6p_full_validation.pdf.gz | 382 KB | Display | |
Data in XML | 1h6p_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1h6p_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/1h6p ftp://data.pdbj.org/pub/pdb/validation_reports/h6/1h6p | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.795, -0.0393, 0.6053), Vector: |
-Components
#1: Protein | Mass: 23667.596 Da / Num. of mol.: 2 / Fragment: DIMERISATION DOMAIN RESIDUES 43-245 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: NUCLEUS / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15554 #2: Chemical | ChemComp-MG / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 51.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7 Details: PH7.0, 15-20% PEG 8000, 100-200 MM MAGNESIUM ACETATE, pH 7.00 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 1999 / 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: 2.2→26.63 Å / Num. obs: 24415 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 43.66 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.231 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 89685 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2.2→23.72 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / ksol: 0.363168 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→23.72 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.24 |