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Yorodumi- PDB-3tq6: Crystal structure of human mitochondrial transcription factor A, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tq6 | ||||||
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Title | Crystal structure of human mitochondrial transcription factor A, TFAM or mtTFA, bound to the light strand promoter LSP | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / Transcription / Transcription regulation / Mitochondrion / DNA-binding / HMGB-UBF_HMG-box / minor groove / tandem HMG boxes / TRANSCRIPTION-DNA complex / mitochondrial nucleoid / light-strand mitochondrial promoter / LSP | ||||||
Function / homology | Function and homology information Mitochondrial transcription initiation / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial respiratory chain complex assembly / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription / DNA binding, bending / mitochondrial nucleoid / Mitochondrial protein degradation / heat shock protein binding ...Mitochondrial transcription initiation / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / mitochondrial respiratory chain complex assembly / mitochondrial promoter sequence-specific DNA binding / mitochondrial transcription / DNA binding, bending / mitochondrial nucleoid / Mitochondrial protein degradation / heat shock protein binding / response to nutrient / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / sequence-specific DNA binding / transcription cis-regulatory region binding / response to hypoxia / mitochondrial matrix / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex / mitochondrion / RNA binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Rubio-Cosials, A. / Sydow, J.F. / Jimenez-Menendez, N. / Fernandez-Millan, P. / Montoya, J. / Jacobs, H.T. / Coll, M. / Bernado, P. / Sola, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Human mitochondrial transcription factor A induces a U-turn structure in the light strand promoter. Authors: Rubio-Cosials, A. / Sidow, J.F. / Jimenez-Menendez, N. / Fernandez-Millan, P. / Montoya, J. / Jacobs, H.T. / Coll, M. / Bernado, P. / Sola, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tq6.cif.gz | 273.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tq6.ent.gz | 214.5 KB | Display | PDB format |
PDBx/mmJSON format | 3tq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/3tq6 ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tq6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 25708.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CR407653.1, TCF6, TCF6L2, TFAM / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q00059 |
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-DNA chain , 2 types, 4 molecules CEDF
#2: DNA chain | Mass: 6659.169 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence occurs naturally in humans. DNA nt 424-445 LSP Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 6909.445 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence occurs naturally in humans. Complementary DNA nt 424-445 LSP Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 4 types, 189 molecules
#4: Chemical | ChemComp-1PE / |
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#5: Chemical | ChemComp-PO4 / |
#6: Chemical | ChemComp-PEG / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.78 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 37.5% (v/v) PEG1000, 300 mM sodium chloride, 0.1 M Na,K-phosphate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2010 Details: Focusing mirrors: one pair of (300x40x15) mm3 long Pt coated Si mirror, 260mm usable, in a Kirkpatrick-Baez geometry; | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: monochromator (horizontally side diffracting Silicon 111 crystal) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→40.84 Å / Num. obs: 28529 / % possible obs: 99.8 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.6 / Redundancy: 7 % / Biso Wilson estimate: 59.217 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.049 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→40.84 Å / Cor.coef. Fo:Fc: 0.9378 / Cor.coef. Fo:Fc free: 0.9137 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 41.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.309 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→40.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.54 Å / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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