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- PDB-1y14: Crystal structure of yeast subcomplex of Rpb4 and Rpb7 -

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Basic information

Entry
Database: PDB / ID: 1y14
TitleCrystal structure of yeast subcomplex of Rpb4 and Rpb7
Components
  • DNA-directed RNA polymerase II 19 kDa polypeptide
  • DNA-directed RNA polymerase II 32 kDa polypeptide
KeywordsTRANSFERASE
Function / homology
Function and homology information


RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Processing of Capped Intron-Containing Pre-mRNA / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / Dual incision in TC-NER / RNA polymerase II, core complex / translation initiation factor binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / P-body / mRNA processing / single-stranded DNA binding / transcription by RNA polymerase II / single-stranded RNA binding / nucleotide binding / nucleus / cytoplasm
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Growth Hormone; Chain: A; / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / HRDC-like superfamily ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / Growth Hormone; Chain: A; / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.3 Å
AuthorsArmache, K.-J. / Mitterweger, S. / Meinhart, A. / Cramer, P.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structures of Complete RNA Polymerase II and Its Subcomplex, Rpb4/7
Authors: Armache, K.-J. / Mitterweger, S. / Meinhart, A. / Cramer, P.
History
DepositionNov 17, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II 32 kDa polypeptide
B: DNA-directed RNA polymerase II 19 kDa polypeptide
C: DNA-directed RNA polymerase II 32 kDa polypeptide
D: DNA-directed RNA polymerase II 19 kDa polypeptide


Theoretical massNumber of molelcules
Total (without water)81,0364
Polymers81,0364
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: DNA-directed RNA polymerase II 32 kDa polypeptide
B: DNA-directed RNA polymerase II 19 kDa polypeptide


Theoretical massNumber of molelcules
Total (without water)40,5182
Polymers40,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-16 kcal/mol
Surface area14860 Å2
MethodPISA
3
C: DNA-directed RNA polymerase II 32 kDa polypeptide
D: DNA-directed RNA polymerase II 19 kDa polypeptide


Theoretical massNumber of molelcules
Total (without water)40,5182
Polymers40,5182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-17 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.646, 114.810, 80.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA-directed RNA polymerase II 32 kDa polypeptide / B32 / Rpb4


Mass: 21436.705 Da / Num. of mol.: 2 / Fragment: residues 35-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P20433, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II 19 kDa polypeptide / B16 / Rpb7


Mass: 19081.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P34087, DNA-directed RNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.37 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementMethod to determine structure: MAD / Resolution: 2.3→20 Å / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.228 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 0 154 4776

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