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- PDB-7bul: Solution structure of the tandem PH and BSD1 domains of TFIIH p62 -

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Basic information

Entry
Database: PDB / ID: 7bul
TitleSolution structure of the tandem PH and BSD1 domains of TFIIH p62
ComponentsGeneral transcription factor IIH subunit 1
KeywordsNUCLEAR PROTEIN / DNA repair factor / general transcription factor / nucleotide excision repair
Function / homology
Function and homology information


transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 ...transcription factor TFIIH holo complex / transcription factor TFIIH core complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / 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 / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / NoRC negatively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / 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 / PH-like domain superfamily
Similarity search - Domain/homology
General transcription factor IIH subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural and dynamical insights into the PH domain of p62 in human TFIIH.
Authors: Okuda, M. / Ekimoto, T. / Kurita, J.I. / Ikeguchi, M. / Nishimura, Y.
History
DepositionApr 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General transcription factor IIH subunit 1


Theoretical massNumber of molelcules
Total (without water)18,3491
Polymers18,3491
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8800 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 18348.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal three residues GSH are artifacts. / Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P32780

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-13C HSQC
132isotropic12D 1H-13C HSQC aromatic
141isotropic23D CBCA(CO)NH
151isotropic23D CBCANH
161isotropic23D HNCO
171isotropic23D HN(CA)CO
181isotropic23D HBHA(CO)NH
191isotropic23D C(CO)NH
1101isotropic23D HN(CO)HB
1111isotropic23D HNHB
1121isotropic23D HN(CO)CG
1131isotropic23D HNCG
1141isotropic13D 1H-15N NOESY
1152isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.2 mM [U-99% 13C; U-99% 15N] TFIIH p62, 90% H2O/10% D2O13C15N_H2O90% H2O/10% D2O
solution20.9 mM [U-99% 13C; U-99% 15N] TFIIH p62, 100% D2O13C15N_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMTFIIH p62[U-99% 13C; U-99% 15N]1
0.9 mMTFIIH p62[U-99% 13C; U-99% 15N]2
Sample conditionsDetails: 20 mM KPB, 5 mM d-DTT / Ionic strength: 20 mM / Label: conditions_1 / pH: 6.8 / Pressure: 1 bar / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III9501
Bruker AVANCE IIIBrukerAVANCE III6002

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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