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Yorodumi- PDB-4j19: Structure of a novel telomere repeat binding protein bound to DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j19 | ||||||
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Title | Structure of a novel telomere repeat binding protein bound to DNA | ||||||
Components |
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Keywords | Transcription/DNA / telomere repeat binding / telomeric DNA / Transcription-DNA complex | ||||||
Function / homology | Function and homology information : / double-stranded telomeric DNA binding / positive regulation of chromatin binding / telomeric DNA binding / : / Cajal body / positive regulation of telomere maintenance via telomerase / PML body / sequence-specific double-stranded DNA binding / sequence-specific DNA binding ...: / double-stranded telomeric DNA binding / positive regulation of chromatin binding / telomeric DNA binding / : / Cajal body / positive regulation of telomere maintenance via telomerase / PML body / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromosome, telomeric region / nuclear body / negative regulation of DNA-templated transcription / centrosome / chromatin / protein-containing complex binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Kappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Lopes Novo, C. / Basquin, C. / Krastev, D.B. / Kittler, R. ...Kappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Lopes Novo, C. / Basquin, C. / Krastev, D.B. / Kittler, R. / Jessberger, R. / Londono-Vallejo, A.J. / Mann, M. / Buchholz, F. | ||||||
Citation | Journal: Embo J. / Year: 2013 Title: HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment. Authors: Kappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Novo, C.L. / Basquin, C. / Araki, M. / Araki, K. / Krastev, D.B. / Kittler, R. / Jessberger, R. / Londono- ...Authors: Kappei, D. / Butter, F. / Benda, C. / Scheibe, M. / Draskovic, I. / Stevense, M. / Novo, C.L. / Basquin, C. / Araki, M. / Araki, K. / Krastev, D.B. / Kittler, R. / Jessberger, R. / Londono-Vallejo, J.A. / Mann, M. / Buchholz, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j19.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j19.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 4j19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j19_validation.pdf.gz | 442.9 KB | Display | wwPDB validaton report |
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Full document | 4j19_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 4j19_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4j19_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/4j19 ftp://data.pdbj.org/pub/pdb/validation_reports/j1/4j19 | HTTPS FTP |
-Related structure data
Related structure data | 2cufS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13102.929 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 233-345 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMBOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NT76 #2: DNA chain | | Mass: 5946.842 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 5677.716 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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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: 3.25 Å3/Da / Density % sol: 62.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 24% PEG 3350, 100 mM sodium acetate, 100 mM potassium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→46.155 Å / Num. obs: 11682 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2CUF Resolution: 2.9→46.155 Å / SU ML: 0.4 / σ(F): 2.01 / Phase error: 24.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→46.155 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 23.6493 Å / Origin y: 28.3987 Å / Origin z: 13.206 Å
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Refinement TLS group | Selection details: all |