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Yorodumi- PDB-1y5o: NMR structure of the amino-terminal domain from the Tfb1 subunit ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y5o | ||||||
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Title | NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH | ||||||
Components | RNA polymerase II transcription factor B 73 kDa subunit | ||||||
Keywords | TRANSCRIPTION / TFIIH / Tfb1 / PH domain / phosphoinositides / VP16 | ||||||
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 / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape ...phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / TP53 Regulates Transcription of DNA Repair Genes / 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 / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / Dual incision in TC-NER / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription by RNA polymerase II / DNA repair / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | SOLUTION NMR / SIMULATED ANNEALING, WITH A COMBINATION OF TORSION ANGLE DYNAMICS, CARTESIAN DYNAMICS. | ||||||
Authors | Di Lello, P. / Nguyen, B.D. / Jones, T.N. / Potempa, K. / Kobor, M.S. / Legault, P. / Omichinski, J.G. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: NMR Structure of the Amino-Terminal Domain from the Tfb1 Subunit of TFIIH and Characterization of Its Phosphoinositide and VP16 Binding Sites Authors: Di Lello, P. / Nguyen, B.D. / Jones, T.N. / Potempa, K. / Kobor, M.S. / Legault, P. / Omichinski, J.G. | ||||||
History |
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Remark 999 | SEQUENCE THE FRAGMENT OF TFB1 STUDIED IN THIS CASE CONTAINS TWO EXTRA RESIDUES (GLY SER) AT THE N- ...SEQUENCE THE FRAGMENT OF TFB1 STUDIED IN THIS CASE CONTAINS TWO EXTRA RESIDUES (GLY SER) AT THE N-TERMINUS AND FOUR EXTRA RESIDUES (GLY ASN SER SER) AT THE C-TERMINUS AS A CONSEQUENCE OF CLONING ARTIFACTS. THESE EXTRA AMINO ACIDS WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND THEREFORE THEY ARE NOT PRESENT IN DEPOSITED STRUCTURES |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y5o.cif.gz | 704.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y5o.ent.gz | 590.5 KB | Display | PDB format |
PDBx/mmJSON format | 1y5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y5o_validation.pdf.gz | 346.3 KB | Display | wwPDB validaton report |
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Full document | 1y5o_full_validation.pdf.gz | 488.9 KB | Display | |
Data in XML | 1y5o_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 1y5o_validation.cif.gz | 64.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/1y5o ftp://data.pdbj.org/pub/pdb/validation_reports/y5/1y5o | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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 / Fragment: sequence database residues 1-115 / 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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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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NMR details | Text: LOWEST ENERGY |
-Sample preparation
Details | Contents: 1.2 MM TFB1 [UNLABELED], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O; 1.2 MM TFB1 [U-15N], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 90% H2O, 10% D2O; 1.2 MM TFB1 [U-15N,13C], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O |
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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 DYNAMICS, CARTESIAN DYNAMICS. Software ordinal: 1 Details: THE THREE-DIMENSIONAL STRUCTURES OF THE AMINO-TERMINAL DOMAIN OF TFB1 WERE DETERMINED USING A SET OF 1208 NOE-DERIVED DISTANCE RESTRAINTS, 124 BACKBONE DIHEDRAL ANGLE (PHI AND PSI) ...Details: THE THREE-DIMENSIONAL STRUCTURES OF THE AMINO-TERMINAL DOMAIN OF TFB1 WERE DETERMINED USING A SET OF 1208 NOE-DERIVED DISTANCE RESTRAINTS, 124 BACKBONE DIHEDRAL ANGLE (PHI AND PSI) RESTRAINTS AND 20 DISTANCE RESTRAINTS FROM HYDROGEN BONDS. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: THE SUBMITTED MODELS ARE THE 20 STRUCTURES WITH NO UPPER BOUND VIOLATION GREATER THAN 0.2 ARMSTRONG, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 2 DEGREES AND ...Conformer selection criteria: THE SUBMITTED MODELS ARE THE 20 STRUCTURES WITH NO UPPER BOUND VIOLATION GREATER THAN 0.2 ARMSTRONG, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 2 DEGREES AND WITH THE LOWEST ENERGIES. Conformers calculated total number: 62 / Conformers submitted total number: 20 |