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- PDB-7dth: Solution structure of RPB6, common subunit of RNA polymerases I, ... -

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Basic information

Entry
Database: PDB / ID: 7dth
TitleSolution structure of RPB6, common subunit of RNA polymerases I, II, and III
ComponentsDNA-directed RNA polymerases I, II, and III subunit RPABC2
KeywordsNUCLEAR PROTEIN / RNA polymerase
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 / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing ...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 / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / 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 / 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 / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
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 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _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: DNA-directed RNA polymerases I, II, and III subunit RPABC2


Theoretical massNumber of molelcules
Total (without water)14,7731
Polymers14,7731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8580 Å2
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic12D 1H-15N HSQC
125isotropic22D 1H-13C HSQC
135isotropic22D 1H-13C HSQC aromatic
144isotropic13D CBCA(CO)NH
154isotropic13D CBCANH
164isotropic13D HNCO
174isotropic13D HN(CA)CO
184isotropic13D HBHA(CO)NH
194isotropic13D HBHANH
1104isotropic13D HN(CO)HB
1114isotropic13D HNHB
1124isotropic13D HN(CO)CG
1134isotropic13D HNCG
1144isotropic13D CC(CO)NH
1154isotropic13D HCC(CO)NH
1165isotropic13D (H)CCH-COSY
1175isotropic13D (H)CCH-TOCSY
1184isotropic13D 1H-15N NOESY
1195isotropic23D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution42.0 mM [U-100% 13C; U-100% 15N] RPB6, 90% H2O/10% D2O13C15N_sample_H2O90% H2O/10% D2O
solution52.0 mM [U-100% 13C; U-100% 15N] RPB6, 100% D2O13C15N_sample_D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2.0 mMRPB6[U-100% 13C; U-100% 15N]4
2.0 mMRPB6[U-100% 13C; U-100% 15N]5
Sample conditionsDetails: 20mM KPB, 5mM d-DTT, 25mM NaCl / Ionic strength: 25 mM / Label: conditions_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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