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Yorodumi- PDB-2gs0: NMR structure of the complex between the PH domain of the Tfb1 su... -
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-Basic information
Entry | Database: PDB / ID: 2gs0 | ||||||
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Title | NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the activation domain of p53 | ||||||
Components |
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Keywords | TRANSCRIPTION / p53 / TFIIH / Tfb1 / activation / PH domain | ||||||
Function / homology | Function and homology information phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate ...phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / mitochondrial DNA repair / T cell lineage commitment / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / negative regulation of DNA replication / ER overload response / B cell lineage commitment / Formation of TC-NER Pre-Incision Complex / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / RNA Polymerase I Promoter Escape / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of release of cytochrome c from mitochondria / transcription by RNA polymerase I / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / Dual incision in TC-NER / DNA damage response, signal transduction by p53 class mediator / response to X-ray / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / T cell proliferation involved in immune response / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Simulated annealing, with a combination of torsion angle, Cartesian dynamics. | ||||||
Authors | Di Lello, P. / Jones, T.N. / Nguyen, B.D. / Legault, P. / Omichinski, J.G. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: Structure of the Tfb1/p53 complex: Insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53. Authors: Di Lello, P. / Jenkins, L.M. / Jones, T.N. / Nguyen, B.D. / Hara, T. / Yamaguchi, H. / Dikeakos, J.D. / Appella, E. / Legault, P. / Omichinski, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gs0.cif.gz | 793.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gs0.ent.gz | 662.8 KB | Display | PDB format |
PDBx/mmJSON format | 2gs0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gs0_validation.pdf.gz | 354.9 KB | Display | wwPDB validaton report |
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Full document | 2gs0_full_validation.pdf.gz | 591.2 KB | Display | |
Data in XML | 2gs0_validation.xml.gz | 59.8 KB | Display | |
Data in CIF | 2gs0_validation.cif.gz | 76.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/2gs0 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/2gs0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 12903.701 Da / Num. of mol.: 1 / Mutation: M1P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TFB1 / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P32776 |
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#2: Protein | Mass: 6018.665 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TP53 / Plasmid: pGEX-2TK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP2 / References: UniProt: P04637 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details |
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Sample conditions | Ionic strength: 20 mM sodium phosphate / pH: 6.5 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Simulated annealing, with a combination of torsion angle, Cartesian dynamics. Software ordinal: 1 Details: The three-dimensional structures of the complex Tfb1/p53 were determined using a set of 1720 NOE-derived distance restraints, 138 backbone dihedral angle (phi and psi) restraints and 26 ...Details: The three-dimensional structures of the complex Tfb1/p53 were determined using a set of 1720 NOE-derived distance restraints, 138 backbone dihedral angle (phi and psi) restraints and 26 distance restraints from hydrogen bonds. Because of the absence of medium-range, long-range and intermolecular NOEs involving residues 20-44 and 59-73 of p53 (chain B), these amino acids were not included in the calculations. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 67 / Conformers submitted total number: 20 |