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- PDB-1a1d: YEAST RNA POLYMERASE SUBUNIT RPB8, NMR, MINIMIZED AVERAGE STRUCTU... -

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Basic information

Entry
Database: PDB / ID: 1a1d
TitleYEAST RNA POLYMERASE SUBUNIT RPB8, NMR, MINIMIZED AVERAGE STRUCTURE, ALPHA CARBONS ONLY
ComponentsRNA POLYMERASE
KeywordsNUCLEOTIDYLTRANSFERASE / RPB8 / RNA POLYMERASE / OB FOLD / EUKARYOTIC / YEAST
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / 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-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribosome biogenesis / transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
RNA polymerase, Rpb8 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsKrapp, S. / Kelly, G. / Reischl, J. / Weinzierl, R. / Matthews, S.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Eukaryotic RNA polymerase subunit RPB8 is a new relative of the OB family.
Authors: Krapp, S. / Kelly, G. / Reischl, J. / Weinzierl, R.O. / Matthews, S.
History
DepositionDec 10, 1997Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)16,5251
Polymers16,5251
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50
Representative

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Components

#1: Protein RNA POLYMERASE / / Coordinate model: Cα atoms only


Mass: 16525.363 Da / Num. of mol.: 1 / Fragment: SUBUNIT RPB8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20436, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: D2O
Sample conditionspH: 6.3 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX500 / Manufacturer: Bruker / Model: DRX500 / Field strength: 500 MHz

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformers calculated total number: 50 / Conformers submitted total number: 1

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