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- PDB-1qkl: hRPABC14.4, essential subunit of human RNA polymerases I, II and III -

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Entry
Database: PDB / ID: 1qkl
TitlehRPABC14.4, essential subunit of human RNA polymerases I, II and III
ComponentsDNA-DIRECTED RNA POLYMERASE II 14.4 KD POLYPEPTIDE
KeywordsRNA POLYMERASE / TRANSCRIPTION
Function / homology
Function and homology information


RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / 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 / Cytosolic sensors of pathogen-associated DNA / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA Polymerase I Transcription Termination ...RNA Polymerase III Chain Elongation / RNA Polymerase III Transcription Termination / 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 / Cytosolic sensors of pathogen-associated DNA / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA Polymerase I Transcription Termination / Viral Messenger RNA Synthesis / MicroRNA (miRNA) biogenesis / Signaling by FGFR2 IIIa TM / 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 / Processing of Capped Intron-Containing Pre-mRNA / PIWI-interacting RNA (piRNA) biogenesis / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / termination of RNA polymerase I transcription / transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / 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 / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase II Transcription Elongation / RNA polymerase I complex / RNA polymerase III complex / Formation of RNA Pol II elongation complex / RNA polymerase II, core complex / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / Inhibition of DNA recombination at telomere / TP53 Regulates Transcription of DNA Repair Genes / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / fibrillar center / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / transcription by RNA polymerase II / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA Polyadenylation / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-directed RNA polymerase activity / Dengue Virus-Host Interactions / Estrogen-dependent gene expression / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / 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 ...: / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsDel Rio-Portilla, F. / Gaskell, A.G. / Gilbert, D. / Ladias, J.A.A. / Wagner, G.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Solution Structure of the Hrpabc14.4 Subunit of Human RNA Polymerases
Authors: Del Rio-Portilla, F. / Gaskell, A.G. / Gilbert, D. / Ladias, J.A.A. / Wagner, G.
History
DepositionJul 26, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Atomic model / Other
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE II 14.4 KD POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)14,4911
Polymers14,4911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 75LEAST RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASE II 14.4 KD POLYPEPTIDE / RPB6


Mass: 14491.026 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: NUCLEUS / Organ: HUMAN FETAL BRAIN / Plasmid: PET-6H2 / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P41584, UniProt: P61218*PLUS, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: VARIOUS TRIPLE RESONANCE & NOES EXPERIMENTS
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE EXPERIMENTS ON 13C AND 15N-LABELED HRPABC14.4

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionspH: 7.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Varian INOVAVarianINOVA5002
Varian INOVAVarianINOVA7503
Bruker AMXBrukerAMX6004

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
Felixstructure solution
XEASYstructure solution
X-PLORstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1 / Details: RESIDUES 801-832 ARE DISORDERED
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 75 / Conformers submitted total number: 22

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