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- PDB-1y1y: RNA Polymerase II-TFIIS-DNA/RNA complex -

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Entry
Database: PDB / ID: 1y1y
TitleRNA Polymerase II-TFIIS-DNA/RNA complex
Components
  • (DNA-directed RNA polymerase II ...) x 7
  • (DNA-directed RNA polymerases I, II, and III ...) x 4
  • 5'-D(P*TP*AP*CP*GP*CP*CP*T)-3'
  • 5'-R(P*AP*GP*GP*C)-3'
  • DNA-directed RNA polymerases I/II/III subunit 10
  • Transcription elongation factor S-II
KeywordsTRANSFERASE/TRANSCRIPTION/DNA-RNA HYBRID / RNA Polymerase II / TFIIS / nucleic acids / transcription / readthrough / TRANSFERASE-TRANSCRIPTION-DNA-RNA HYBRID COMPLEX
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / 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 complex recruiting activity / regulation of mRNA 3'-end processing / 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 / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / 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 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / 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 / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription antitermination / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / peroxisome / single-stranded DNA binding / ribosome biogenesis / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / nucleotide binding / mRNA binding / regulation of transcription by RNA polymerase II / nucleolus / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. ...Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / TFIIS/LEDGF domain 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
Similarity search - Domain/homology
DNA / RNA / DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor S-II / 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 / RNA / DNA-directed RNA polymerase II subunit RPB1 / Transcription elongation factor S-II / 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 Å
AuthorsCramer, P. / Kettenberger, H. / Armache, K.-J.
CitationJournal: Mol.Cell / Year: 2004
Title: Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.
Authors: Kettenberger, H. / Armache, K.J. / Cramer, P.
History
DepositionNov 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
T: 5'-D(P*TP*AP*CP*GP*CP*CP*T)-3'
P: 5'-R(P*AP*GP*GP*C)-3'
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
D: DNA-directed RNA polymerase II 32 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
G: DNA-directed RNA polymerase II 19 kDa polypeptide
H: DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
I: DNA-directed RNA polymerase II subunit 9
J: DNA-directed RNA polymerases I/II/III subunit 10
K: DNA-directed RNA polymerase II 13.6 kDa polypeptide
L: DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
S: Transcription elongation factor S-II


Theoretical massNumber of molelcules
Total (without water)537,78315
Polymers537,78315
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)220.2, 395.7, 282.1
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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DNA-directed RNA polymerase II ... , 7 types, 7 molecules ABCDGIK

#3: Protein DNA-directed RNA polymerase II largest subunit / RNA polymerase II subunit 1 / 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) / References: UniProt: P04050, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase II 140 kDa polypeptide / B150 / RNA polymerase II subunit 2 / 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) / References: UniProt: P08518, DNA-directed RNA polymerase
#5: Protein DNA-directed RNA polymerase II 45 kDa polypeptide / 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) / References: UniProt: P16370, DNA-directed RNA polymerase
#6: Protein DNA-directed RNA polymerase II 32 kDa polypeptide / B32 / Coordinate model: Cα atoms only


Mass: 25451.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20433, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase II 19 kDa polypeptide / B16 / Coordinate model: Cα atoms only


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34087, DNA-directed RNA polymerase
#11: Protein DNA-directed RNA polymerase II subunit 9 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / B12.6 / 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) / References: UniProt: P27999, DNA-directed RNA polymerase
#13: Protein DNA-directed RNA polymerase II 13.6 kDa polypeptide / 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) / References: UniProt: P38902, DNA-directed RNA polymerase

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DNA-directed RNA polymerases I, II, and III ... , 4 types, 4 molecules EFHL

#7: Protein DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide / 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) / References: UniProt: P20434, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide / ABC23 / 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) / References: UniProt: P20435, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide / ABC14.4 / 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) / References: UniProt: P20436, DNA-directed RNA polymerase
#14: Protein DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide / ABC10-alpha / 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) / References: UniProt: P40422, DNA-directed RNA polymerase

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Protein , 2 types, 2 molecules JS

#12: Protein DNA-directed RNA polymerases I/II/III subunit 10 / DNA- directed RNA polymerases I / II / and III 8.3 kDa polypeptide / ABC10- beta / ABC8 / 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) / References: UniProt: P22139, DNA-directed RNA polymerase
#15: Protein Transcription elongation factor S-II / DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway ...DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway regulatory protein 2 / Coordinate model: Cα atoms only


Mass: 20271.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DST1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / References: UniProt: P07273

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DNA chain / RNA chain , 2 types, 2 molecules TP

#1: DNA chain 5'-D(P*TP*AP*CP*GP*CP*CP*T)-3' / Coordinate model: P atoms only


Mass: 2073.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide
#2: RNA chain 5'-R(P*AP*GP*GP*C)-3' / Coordinate model: P atoms only


Mass: 1279.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic oligonucleotide

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.71 Å3/Da / Density % sol: 78.47 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9919 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 103460 / Num. obs: 103460 / % possible obs: 98.7 % / Observed criterion σ(F): 20.3 / Observed criterion σ(I): 20.3 / Redundancy: 4.3 % / Rsym value: 0.07

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→50 Å / σ(F): 5.4 / Stereochemistry target values: Engh & Huber
Details: The coordinates for only the alpha carbons and phosphorus atoms are present in the structure. The number of missing atoms was so much that remark 470 for the missing atoms list were removed.
RfactorNum. reflectionSelection details
Rwork0.281 --
all-103460 -
obs-103460 -
Rfree--RANDOM
Refinement stepCycle: LAST / Resolution: 4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4101 11 0 0 4112

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