[English] 日本語
Yorodumi
- PDB-1sfo: RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sfo
TitleRNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX
Components
  • (DNA-directed RNA polymerase II ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III ...RNA polymerase) x 5
  • DNA STRANDDNA
  • RNA STRAND
KeywordsTRANSCRIPTION/DNA-RNA HYBRID / TRANSCRIPTION / MRNA / MULTIPROTEIN COMPLEX / MOLECULAR MACHINE / DNA / TRANSCRIPTION-DNA-RNA HYBRID COMPLEX
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening ...RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase II activity / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase II transcription / Dual incision in TC-NER / transcription by RNA polymerase I / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / translesion synthesis / transcription-coupled nucleotide-excision repair / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / transcription, RNA-templated / cytoplasmic stress granule / transcription initiation from RNA polymerase II promoter / 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 / Enzyme I; Chain A, domain 2 / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 ...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 / Enzyme I; Chain A, domain 2 / Hypothetical Protein Ta0175; Chain: A, domain 2 / Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Topoisomerase I; Chain A, domain 4 / RNA polymerase Rpb2, domain 2 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / 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 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA Polymerase Alpha Subunit; Chain A, domain 2 / N-terminal domain of TfIIb / Rubrerythrin, domain 2 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, Rpb5, N-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb8 / RNA polymerase subunit 9 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / : / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, subunit H/Rpb5 C-terminal / : / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Zinc finger TFIIS-type profile. / Transcription factor S-II (TFIIS) / C2C2 Zinc finger / Zinc finger, TFIIS-type / Gyrase A; domain 2 / Homeodomain-like / RNA polymerase Rpb1, domain 3 superfamily / : / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 / RNA polymerase I subunit A N-terminus / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4
Similarity search - Domain/homology
RNA / DNA (> 10) / DNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / 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 ...RNA / DNA (> 10) / DNA / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / 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 RPB11 / 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: 3.61 Å
AuthorsWestover, K.D. / Bushnell, D.A. / Kornberg, R.D.
CitationJournal: Science / Year: 2004
Title: Structural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II
Authors: Westover, K.D. / Bushnell, D.A. / Kornberg, R.D.
History
DepositionFeb 20, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMar 2, 2004ID: 1R9R
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: RNA STRAND
T: DNA STRAND
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)477,65321
Polymers477,10612
Non-polymers5489
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)167.076, 221.256, 193.685
Angle α, β, γ (deg.)90.00, 100.10, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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

#3: Protein DNA-directed RNA polymerase II largest subunit / 2.7.7.6


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
#4: Protein DNA-directed RNA polymerase II 140 kDa polypeptide / 2.7.7.6


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
#5: Protein DNA-directed RNA polymerase II 45 kDa polypeptide / 2.7.7.6


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
#9: Protein DNA-directed RNA polymerase II 14.2 kDa polypeptide / 2.7.7.6


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
#11: Protein DNA-directed RNA polymerase II 13.6 kDa polypeptide / 2.7.7.6


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

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

#6: Protein DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide / RNA polymerase / 2.7.7.6


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
#7: Protein DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide / RNA polymerase / 2.7.7.6


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
#8: Protein DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide / RNA polymerase / 2.7.7.6


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
#10: Protein DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide / RNA polymerase / 2.7.7.6


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
#12: Protein DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide / RNA polymerase / 2.7.7.6


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

-
RNA chain / DNA chain , 2 types, 2 molecules RT

#1: RNA chain RNA STRAND


Mass: 3264.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TRANSCRIPT
#2: DNA chain DNA STRAND / DNA


Mass: 4215.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TEMPLATE

-
Non-polymers , 2 types, 9 molecules

#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#14: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, ammonium sodium phosphate, DTT, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 600011
2ammonium sodium phosphate11
3DTT11
4H2O11
5PEG 600012
6ammonium sodium phosphate12
7DTT12
8H2O12
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, sitting drop / Details: Gnatt, A.L., (2001) Science, 292, 1876.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMdioxane1reservoir
210 mMdithiothreitol1reservoir
3390 mM1reservoir(NH4)2HPO4/NaH2PO4
55-8 mgprotein1drop
4PEG60001reservoir
61
71
81

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→40 Å / Num. obs: 73591 / % possible obs: 92.9 % / Redundancy: 2.5 %
Reflection shellResolution: 3.6→3.7 Å / Rmerge(I) obs: 0.312 / % possible all: 87.1
Reflection
*PLUS
Highest resolution: 3.6 Å / Lowest resolution: 40 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.139
Reflection shell
*PLUS
Highest resolution: 3.6 Å / Lowest resolution: 3.7 Å / % possible obs: 87.1 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I6H
Resolution: 3.61→39.86 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 63989.39 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.343 7393 10 %RANDOM
Rwork0.315 ---
all0.32 ---
obs0.315 73591 92.7 %-
Displacement parametersBiso mean: 40.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.6 Å20 Å2-5.54 Å2
2---4.22 Å20 Å2
3----5.38 Å2
Refinement stepCycle: LAST / Resolution: 3.61→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28142 496 9 0 28647
LS refinement shellResolution: 3.61→3.83 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 1067 9.8 %
Rwork0.391 9803 -
obs--81.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3DNA-RNA.PARAMDNA-RNA.TOP

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more