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- PDB-1y5o: NMR structure of the amino-terminal domain from the Tfb1 subunit ... -

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Basic information

Entry
Database: PDB / ID: 1y5o
TitleNMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH
ComponentsRNA polymerase II transcription factor B 73 kDa subunit
KeywordsTRANSCRIPTION / 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 holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape ...phosphatidylinositol-5-phosphate binding / nucleotide-excision repair factor 3 complex / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / 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 / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / transcription by RNA polymerase II / DNA repair / nucleus / cytosol
Similarity search - Function
TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like ...TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit TFB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / SIMULATED ANNEALING, WITH A COMBINATION OF TORSION ANGLE DYNAMICS, CARTESIAN DYNAMICS.
AuthorsDi Lello, P. / Nguyen, B.D. / Jones, T.N. / Potempa, K. / Kobor, M.S. / Legault, P. / Omichinski, J.G.
CitationJournal: 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
DepositionDec 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Remark 999SEQUENCE 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II transcription factor B 73 kDa subunit


Theoretical massNumber of molelcules
Total (without water)12,9041
Polymers12,9041
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 62THE 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.
RepresentativeModel #1

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Components

#1: Protein RNA polymerase II transcription factor B 73 kDa subunit / TFB1


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

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-EDITED NOESY -HSQC
1312D 1H-15N HSQC
1413D 13C- EDITED HMQC-NOESY
NMR detailsText: LOWEST ENERGY

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Sample preparation

DetailsContents: 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
Sample conditionsIonic strength: 20 mM SODIUM PHOSPHATE / pH: 6.5 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian UNITYVarianUNITY6002
Varian UNITYVarianUNITY8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE- KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
VNMR 6.1.C6.1.Cstructure solution
NMRPipe2.2structure solution
NMRView5.0.4structure solution
CNS1structure solution
RefinementMethod: 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 ensembleConformer 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

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