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- PDB-1twf: RNA polymerase II complexed with UTP at 2.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 1twf
TitleRNA polymerase II complexed with UTP at 2.3 A resolution
Components
  • (DNA-directed RNA polymerase II ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III ...RNA polymerase) x 5
KeywordsTRANSCRIPTION / MRNA / MULTIPROTEIN COMPLEX / MOLECULAR MACHINE / ZINC MOTIFS
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase III transcription ...RNA Polymerase I Transcription Initiation / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase III transcription / RNA polymerase II activity / transcription initiation from RNA polymerase III promoter / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA polymerase I activity / termination of RNA polymerase I transcription / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / tRNA transcription by RNA polymerase III / RNA Polymerase I Promoter Escape / transcription elongation from RNA polymerase I promoter / RNA Polymerase II Pre-transcription Events / transcription initiation from RNA polymerase I promoter / transcription by RNA polymerase I / transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / translesion synthesis / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / transcription elongation from RNA polymerase II promoter / transcription initiation from RNA polymerase II promoter / ribonucleoside binding / transcription by RNA polymerase II / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / transcription, RNA-templated / ribosome biogenesis / nucleic acid binding / protein dimerization activity / mRNA binding / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / RNA polymerase alpha subunit dimerisation domain / DCoH-like / Hypothetical Protein Ta0175; Chain: A, domain 2 / Enzyme I; Chain A, domain 2 / RNA polymerase, Rpb5, N-terminal domain ...Gyrase A; domain 2 - #140 / RNA polymerase ii / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1 funnel domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / RNA polymerase alpha subunit dimerisation domain / DCoH-like / Hypothetical Protein Ta0175; Chain: A, domain 2 / Enzyme I; Chain A, domain 2 / RNA polymerase, Rpb5, N-terminal domain / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, subunit 2, domain 6 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / RNA polymerase II, Rpb2 subunit, wall domain / N-terminal domain of TfIIb - #10 / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 7 superfamily / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerase subunit RPB10 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase subunit 9 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb3/Rpb11 dimerisation domain / : / RNA polymerase Rpb5, C-terminal domain / DNA-directed RNA polymerase, RBP11-like dimerisation domain / : / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / C2C2 Zinc finger / Zinc finger TFIIS-type profile. / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Gyrase A; domain 2 / Homeodomain-like / Single Sheet / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 4
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / : / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 ...DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / : / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / URIDINE 5'-TRIPHOSPHATE / DNA-directed RNA polymerases I, II, and III subunit RPABC4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWestover, K.D. / Bushnell, D.A. / Kornberg, R.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
Authors: Westover, K.D. / Bushnell, D.A. / Kornberg, R.D.
History
DepositionJun 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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 RNA polymerase II 140 kDa polypeptide
C: DNA-directed RNA polymerase II 45 kDa 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
H: DNA-directed RNA polymerases I, II, and III 14.5 kDa 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 kDa polypeptide
L: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,74321
Polymers469,62610
Non-polymers1,11711
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: DNA-directed RNA polymerase II largest subunit
B: DNA-directed RNA polymerase II 140 kDa polypeptide
C: DNA-directed RNA polymerase II 45 kDa 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
H: DNA-directed RNA polymerases I, II, and III 14.5 kDa 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 kDa polypeptide
L: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
hetero molecules

A: DNA-directed RNA polymerase II largest subunit
B: DNA-directed RNA polymerase II 140 kDa polypeptide
C: DNA-directed RNA polymerase II 45 kDa 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
H: DNA-directed RNA polymerases I, II, and III 14.5 kDa 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 kDa polypeptide
L: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)941,48742
Polymers939,25220
Non-polymers2,23522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area119300 Å2
ΔGint-690 kcal/mol
Surface area283230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123, 223, 374
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

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DNA-directed RNA polymerase II ... , 5 types, 5 molecules ABCIK

#1: Protein DNA-directed RNA polymerase II largest subunit / B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P04050, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase II 140 kDa polypeptide / B150 / RNA polymerase II subunit 2


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P08518, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase II 45 kDa polypeptide / B44.5


Mass: 35330.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P16370, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase II 14.2 kDa polypeptide / B12.6


Mass: 14308.161 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P27999, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase II 13.6 kDa polypeptide / B13.6


Mass: 13633.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P38902, DNA-directed RNA polymerase

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

#4: Protein DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide / RNA polymerase / ABC27


Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20434, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide / RNA polymerase / ABC23


Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20435, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide / RNA polymerase / ABC14.4


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P20436, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide / RNA polymerase / ABC10-beta / ABC8


Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P22139, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide / RNA polymerase / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (baker's yeast) / Strain: DELTA-RPB4 / References: UniProt: P40422, DNA-directed RNA polymerase

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Non-polymers , 3 types, 11 molecules

#11: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#12: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#13: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM

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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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, AMMONIUM HYDROGEN PHOSPHATE, SODIUM DIHYDROGEN PHOSPHATE, DIOXANE, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979
DetectorDetector: CCD / Date: Aug 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 258084

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I50
Resolution: 2.3→40 Å
RfactorNum. reflection
Rfree0.294 -
Rwork0.247 -
all0.26 -
obs0.26 258084
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28279 0 39 0 28318

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