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- PDB-1pfj: Solution structure of the N-terminal PH/PTB domain of the TFIIH P... -

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Entry
Database: PDB / ID: 1pfj
TitleSolution structure of the N-terminal PH/PTB domain of the TFIIH P62 subunit
ComponentsTFIIH basal transcription factor complex p62 subunit
KeywordsTRANSCRIPTION / PH/PTB domain / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


transcription factor TFIIH holo complex / transcription factor TFIIH core complex / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation ...transcription factor TFIIH holo complex / transcription factor TFIIH core complex / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / RNA Polymerase I Transcription Initiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / hormone-mediated signaling pathway / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase II / DNA repair / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm
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 factor IIH subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsGervais, V. / Lamour, V. / Jawhari, A. / Frindel, F. / Wasielewski, E. / Thierry, J.C. / Kieffer, B. / Poterszman, A. / Structural Proteomics in Europe (SPINE)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: TFIIH contains a PH domain involved in DNA nucleotide excision repair.
Authors: Gervais, V. / Lamour, V. / Jawhari, A. / Frindel, F. / Wasielewski, E. / Dubaele, S. / Egly, J.M. / Thierry, J.C. / Kieffer, B. / Poterszman, A.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: TFIIH basal transcription factor complex p62 subunit


Theoretical massNumber of molelcules
Total (without water)12,3061
Polymers12,3061
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 60structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein TFIIH basal transcription factor complex p62 subunit / Basic transcription factor 62 kDa subunit / BTF2-p62 / General transcription factor IIH polypeptide 1


Mass: 12306.316 Da / Num. of mol.: 1 / Fragment: N-terminal PH/PTB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1 OR BTF2 / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32780

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
4142D NOESY
1213D 13C-separated NOESY
2323D 15N-separated NOESY
242HNHA
353IPAP-[1H-15N] HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM P62 U-15N,13C; 20mM deuterated TRIS; 90% H2O, 10% D2O90% H2O/10% D2O
21.2mM P62 U-15N; 20mM deuterated TRIS; 90% H2O, 10% D2O90% H2O/10% D2O
30.9mM P62 U-15N; 20mM deuterated TRIS + 26ug C12E6/hexanol; 90% H2O, 10% D2O90% H2O, 10% D2O; 26 ug C12E6/hexanol
41.5mM P62; 20mM deuterated TRIS; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM 7.4 ambient 293 K
220mM 7.4 ambient 293 K
320mM 7.4 ambient 298 K
420mM 7.4 ambient 293 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
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORNIHBrungerrefinement
CNS1Brungerstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: total NOE restraints: 1944 dihedral angle restraints: 148 hydrogen bonds: 35 Residual Dipolar coupling: 76
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 19

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