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- PDB-1nt9: Complete 12-subunit RNA polymerase II -

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Basic information

Entry
Database: PDB / ID: 1nt9
TitleComplete 12-subunit RNA polymerase II
Components
  • (DNA-DIRECTED RNA POLYMERASE II ...) x 5
  • (DNA-directed RNA polymerases I, II, and III ...) x 5
  • DNA-directed polymerase II SECOND LARGEST SUBUNIT
  • YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDE
KeywordsTRANSCRIPTION / TRANSFERASE / DNA-dependent RNA polymerase / cellular RNA polymerase / multisubunit complex / gene expression / mRNA / messenger RNA synthesis
Function / homology
Function and homology information


RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription ...RPB4-RPB7 complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 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 / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / 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 / termination of RNA polymerase III transcription / 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 / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / positive regulation of translational initiation / transcription by RNA polymerase III / Dual incision in TC-NER / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / single-stranded DNA binding / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily ...DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Zinc finger TFIIS-type signature. / 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 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / : / RNA polymerase, Rpb8 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / 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. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 ...DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsArmache, K.-J. / Kettenberger, H. / Cramer, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Architecture of initiation-competent 12-subunit RNA polymerase II
Authors: Armache, K.-J. / Kettenberger, H. / Cramer, P.
History
DepositionJan 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
B: DNA-directed polymerase II SECOND LARGEST SUBUNIT
C: DNA-directed RNA polymerase II 45 kDa polypeptide
D: YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDE
E: DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
F: DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
G: DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KD POLYPEPTIDE
I: DNA-directed RNA polymerase II 14.2 kDa polypeptide
J: DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide
K: DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE
L: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide


Theoretical massNumber of molelcules
Total (without water)514,15812
Polymers514,15812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.4, 391.4, 282.2
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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DNA-DIRECTED RNA POLYMERASE II ... , 5 types, 5 molecules ACGIK

#1: Protein DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT / E.C.2.7.7.6 / Rpb1 / B220 / Coordinate model: Cα atoms only


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P04050, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II 45 kDa polypeptide / E.C.2.7.7.6 / Rpb3 / B44.5 / Coordinate model: Cα atoms only


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P16370, DNA-directed RNA polymerase
#7: Protein DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDE / E.C.2.7.7.6 / Rpb7 / B16 / Rpb7p / Coordinate model: Cα atoms only


Mass: 19081.053 Da / Num. of mol.: 1
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
#9: Protein DNA-directed RNA polymerase II 14.2 kDa polypeptide / E.C.2.7.7.6 / Rpb9 / B12.6 / Rpb9p / Coordinate model: Cα atoms only


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P27999, DNA-directed RNA polymerase
#11: Protein DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDE / E.C.2.7.7.6 / Rpb11 / B13.6 / Coordinate model: Cα atoms only


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P38902, DNA-directed RNA polymerase

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Protein , 2 types, 2 molecules BD

#2: Protein DNA-directed polymerase II SECOND LARGEST SUBUNIT / E.C.2.7.7.6 / Rpb2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide / Coordinate model: Cα atoms only


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P08518, DNA-directed RNA polymerase
#4: Protein YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDE / E.C.2.7.7.6 / Rpb4 / B32 / Coordinate model: Cα atoms only


Mass: 25451.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Numbering of resiudes D10-D24 is arbitrary
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P20433, DNA-directed RNA polymerase

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DNA-directed RNA polymerases I, II, and III ... , 5 types, 5 molecules EFHJL

#5: Protein DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide / E.C.2.7.7.6 / Rpb5 / ABC27 / Coordinate model: Cα atoms only


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P20434, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide / E.C.2.7.7.6 / Rpb6 / ABC23 / RNA polymerase II sixth subunit / Coordinate model: Cα atoms only


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P20435, DNA-directed RNA polymerase
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KD POLYPEPTIDE / E.C.2.7.7.6 / Rpb8 / ABC14.4 / 16-kDa RNA polymerase subunit / Coordinate model: Cα atoms only


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P20436, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide / E.C.2.7.7.6 / Rpb10 / ABC10-beta / ABC8 / Rpb10p / Coordinate model: Cα atoms only


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P22139, DNA-directed RNA polymerase
#12: Protein DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide / E.C.2.7.7.6 / Rpb12 / ABC10-alpha / Rpc10p / Coordinate model: Cα atoms only


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: delta-Rpb4 / References: UniProt: P40422, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.92 Å3/Da / Density % sol: 79.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 20000, ammonium sodium phosphate, sodium chloride, dioxane, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
28 %PEG200001reservoir
3360 mMsodium ammonium phosphate1reservoirpH6.0
450 mMdioxane1reservoir
55 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9185 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9185 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. all: 83431 / Num. obs: 83431 / % possible obs: 93.8 % / Rsym value: 0.093
Reflection shellResolution: 4.2→4.35 Å / Rmerge(I) obs: 0.363 / % possible all: 89.5
Reflection
*PLUS
Highest resolution: 4.2 Å / Lowest resolution: 50 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.093
Reflection shell
*PLUS
Highest resolution: 4.2 Å / % possible obs: 89.5 % / Num. unique obs: 7893

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
Omodel building
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I6H

1i6h


Resolution: 4.2→50 Å / σ(F): 0
Details: Model was fitted into electron densities, no least square minimization was performed
Num. reflection% reflection
all83431 -
obs83431 93.8 %
Refinement stepCycle: LAST / Resolution: 4.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 0 0 3779
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg

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