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- PDB-2f3i: Solution Structure of a Subunit of RNA Polymerase II -

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Basic information

Entry
Database: PDB / ID: 2f3i
TitleSolution Structure of a Subunit of RNA Polymerase II
ComponentsDNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptideRNA polymerase
KeywordsTRANSFERASE / RNA Polymerase II
Function / homology
Function and homology information


transcription initiation from RNA polymerase I promoter / transcription elongation from RNA polymerase I promoter / positive regulation of viral transcription / termination of RNA polymerase I transcription / snRNA transcription by RNA polymerase II / positive regulation of gene expression, epigenetic / RNA metabolic process / somatic stem cell population maintenance / RNA polymerase I complex / RNA polymerase III complex ...transcription initiation from RNA polymerase I promoter / transcription elongation from RNA polymerase I promoter / positive regulation of viral transcription / termination of RNA polymerase I transcription / snRNA transcription by RNA polymerase II / positive regulation of gene expression, epigenetic / RNA metabolic process / somatic stem cell population maintenance / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription by RNA polymerase III / 7-methylguanosine mRNA capping / positive regulation of type I interferon production / transcription elongation from RNA polymerase II promoter / DNA-directed 5'-3' RNA polymerase activity / regulation of gene silencing by miRNA / fibroblast growth factor receptor signaling pathway / mRNA splicing, via spliceosome / transcription-coupled nucleotide-excision repair / single-stranded DNA binding / protein-DNA complex / transcription by RNA polymerase II / transcription initiation from RNA polymerase II promoter / transcription, DNA-templated / nucleoplasm / nucleus / cytosol
RNA polymerase Rpb8 / Nucleic acid-binding, OB-fold / RNA polymerase, Rpb8 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
DNA-directed RNA polymerases I, II, and III subunit RPABC3
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model type detailsminimized average
AuthorsKang, X. / Jin, C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural, biochemical, and dynamic characterizations of the hRPB8 subunit of human RNA polymerases
Authors: Kang, X. / Hu, Y. / Li, Y. / Guo, X. / Jiang, X. / Lai, L. / Xia, B. / Jin, C.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide


Theoretical massNumber of molelcules
Total (without water)17,1621
Polymers17,1621
Non-polymers00
Water0
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide / RNA polymerase / RNA Polymerase II Subunit / RPB17 / RPB8 / RPABC3


Mass: 17162.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / References: UniProt: P52434, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment

Conditions-ID: 1 / Solution-ID: 1

Experiment-IDType
13D 13C-separated NOESY
23D 15N-separated NOESY
32D 15N-edited HSQC
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques.

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Sample preparation

DetailsContents: 0.5mM RNA Polymerase II Subunit U-15N,13C
Solvent system: 20mM potassium phosphate buffer, 10mM DTT; 90% H2O, 10% D2O
Sample conditionsIonic strength: 50mM / pH: 6.3 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer

Manufacturer: Bruker / Model: Avance / Type: Bruker Avance

Field strength (MHz)Spectrometer-ID
8001
5002

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Processing

NMR software
NameVersionDeveloperClassification
XWINNMR3.5Brukercollection
NMRPipe2.1Frank Delaglioprocessing
NMRView5Bruce Johnsondata analysis
CYANA1.0.6Peter Gunterstructure solution
AMBER7David Caserefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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