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Basic information

Entry
Database: PDB / ID: 7dti
TitleSolution structure of the complex between RNA polymerase subunit RPB6 and TFIIH p62 PH domain
Components
  • DNA-directed RNA polymerases I, II, and III subunit RPABC2
  • General transcription factor IIH subunit 1
KeywordsNUCLEAR PROTEIN / RNA polymerase / general transcription factor
Function / homology
Function and homology information


RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / Abortive elongation of HIV-1 transcript in the absence of Tat ...RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / Viral Messenger RNA Synthesis / 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 / PIWI-interacting RNA (piRNA) biogenesis / 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 / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / 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 / DNA-directed RNA polymerase, subunit RPB6 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit ...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 / DNA-directed RNA polymerase, subunit RPB6 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / PH-like domain superfamily
Similarity search - Domain/homology
General transcription factor IIH subunit 1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsOkuda, M. / Nishimura, Y.
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Three human RNA polymerases interact with TFIIH via a common RPB6 subunit.
Authors: Okuda, M. / Suwa, T. / Suzuki, H. / Yamaguchi, Y. / Nishimura, Y.
History
DepositionJan 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1May 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: DNA-directed RNA polymerases I, II, and III subunit RPABC2
B: General transcription factor IIH subunit 1


Theoretical massNumber of molelcules
Total (without water)27,3622
Polymers27,3622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA- ...RNA polymerases I / II / and III subunit ABC2 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I / and III 14.4 kDa polypeptide / RPABC14.4 / RPB14.4 / RPB6 homolog / RPC15


Mass: 14773.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLR2F, POLRF / Production host: Escherichia coli (E. coli) / References: UniProt: P61218
#2: Protein General transcription factor IIH subunit 1


Mass: 12588.593 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K6V299

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
1143isotropic22D 1H-15N HSQC
122isotropic22D 1H-13C HSQC
1154isotropic22D 1H-13C HSQC
132isotropic22D 1H-13C HSQC aromatic
1164isotropic22D 1H-13C HSQC aroma
141isotropic13D CBCA(CO)NH
1173isotropic13D CBCA(CO)NH
151isotropic13D CBCANH
1183isotropic13D CBCANH
161isotropic13D HNCO
1193isotropic13D HNCO
171isotropic13D HN(CA)CO
1203isotropic13D HN(CA)CO
1101isotropic13D HNCA
1213isotropic13D HNCA
1111isotropic13D HN(CO)CA
1223isotropic13D HN(CO)CA
181isotropic13D HBHA(CO)NH
1233isotropic13D HBHA(CO)NH
191isotropic13D HBHANH
1243isotropic13D HBHANH
1121isotropic23D 1H-15N NOESY
1253isotropic23D 1H-15N NOESY
1132isotropic23D 1H-13C NOESY
1264isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.38 mM [U-100% 13C; U-100% 15N] RPB6, 0.38 mM TFIIH p62, 90% H2O/10% D2O13C15N_RPB6-p62_H2O90% H2O/10% D2O
solution20.38 mM [U-100% 13C; U-100% 15N] RPB6, 0.38 mM TFIIH p62, 100% D2O13C15N_RPB6-p62_D2O100% D2O
solution30.38 mM [U-100% 13C; U-100% 15N] TFIIH p62, 0.38 mM RPB6, 90% H2O/10% D2O13C15N_p62-RPB6_H2O90% H2O/10% D2O
solution40.38 mM [U-100% 13C; U-100% 15N] TFIIH p62, 0.38 mM RPB6, 100% D2O13C15N_p62-RPB6_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.38 mMRPB6[U-100% 13C; U-100% 15N]1
0.38 mMTFIIH p62natural abundance1
0.38 mMRPB6[U-100% 13C; U-100% 15N]2
0.38 mMTFIIH p62natural abundance2
0.38 mMTFIIH p62[U-100% 13C; U-100% 15N]3
0.38 mMRPB6natural abundance3
0.38 mMTFIIH p62[U-100% 13C; U-100% 15N]4
0.38 mMRPB6natural abundance4
Sample conditionsDetails: 20mM KPB, 5mM d-DTT, 25mM NaCl / Ionic strength: 25 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE III HDBrukerAVANCE III HD9502

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Processing

NMR software
NameDeveloperClassification
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificpeak picking
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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