[English] 日本語
Yorodumi
- PDB-5fmf: the P-lobe of RNA polymerase II pre-initiation complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fmf
Titlethe P-lobe of RNA polymerase II pre-initiation complex
Components
  • (DNA REPAIR HELICASE ...) x 2
  • (DNA-DIRECTED RNA POLYMERASE II SUBUNIT ...Polymerase) x 6
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ...RNA polymerase) x 5
  • (RNA POLYMERASE II PRE-INITIATION COMPLEX, ...) x 3
  • (RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT ...) x 2
  • (TRANSCRIPTION INITIATION FACTOR ...) x 5
  • NON-TEMPLATE STRAND DNA
  • TATA-BOX-BINDING PROTEIN, TBP
  • TEMPLATE STRAND DNA
  • TRANSCRIPTION ELONGATION FACTOR S-II, DST1
KeywordsTRANSCRIPTION / PRE-INITIATION COMPLEX / RNA POLYMERASE / TFIIE / TFIIH / TFIIB / TBP / TFIIF / PROTEIN
Function / homology
Function and homology information


regulation of transposition, RNA-mediated / regulation of mitotic recombination / regulation of mRNA 3'-end processing / RNA polymerase II complex recruiting activity / promoter clearance from RNA polymerase II promoter / TFIIA-class transcription factor complex binding / dephosphorylation of RNA polymerase II C-terminal domain / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination ...regulation of transposition, RNA-mediated / regulation of mitotic recombination / regulation of mRNA 3'-end processing / RNA polymerase II complex recruiting activity / promoter clearance from RNA polymerase II promoter / TFIIA-class transcription factor complex binding / dephosphorylation of RNA polymerase II C-terminal domain / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / positive regulation of mitotic recombination / RNA polymerase III transcription regulatory region sequence-specific DNA binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / RNA polymerase I general transcription initiation factor binding / TFIIF-class transcription factor complex binding / regulation of protein serine/threonine phosphatase activity / transcription factor TFIIH core complex / DNA translocase activity / transcription factor TFIIH holo complex / transcription factor TFIIF complex / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / transcription elongation from RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / phosphorylation of RNA polymerase II C-terminal domain / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / DNA duplex unwinding / RNA polymerase I preinitiation complex assembly / general transcription initiation factor activity / 5'-3' DNA helicase activity / nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / 3'-5' DNA helicase activity / mRNA export from nucleus in response to heat stress / poly(A)+ mRNA export from nucleus / RNA polymerase II preinitiation complex assembly / positive regulation of transcription regulatory region DNA binding / DNA binding, bending / RNA Polymerase I Transcription Initiation / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / termination of RNA polymerase III transcription / ATPase activator activity / RNA polymerase II general transcription initiation factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of TC-NER Pre-Incision Complex / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II activity / transcription factor TFIID complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase II complex binding / protein phosphatase activator activity / positive regulation of translational initiation / RNA polymerase I activity / Gap-filling DNA repair synthesis and ligation in TC-NER / Dual incision in TC-NER / RNA Polymerase II Transcription Elongation / tRNA transcription by RNA polymerase III / RNA Polymerase I Promoter Escape / Estrogen-dependent gene expression / RNA Polymerase II Pre-transcription Events / transcription by RNA polymerase I / termination of RNA polymerase II transcription / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription preinitiation complex / RNA polymerase II core promoter sequence-specific DNA binding / ATP-dependent activity, acting on DNA / transcription antitermination / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / response to UV / translation initiation factor binding / transcription elongation from RNA polymerase II promoter / TBP-class protein binding / nucleotide-excision repair / positive regulation of RNA polymerase II transcription preinitiation complex assembly / nucleotide-excision repair, DNA duplex unwinding / positive regulation of transcription elongation from RNA polymerase II promoter / P-body / nucleotide-excision repair, preincision complex assembly / ribonucleoside binding / DNA-templated transcription, initiation / DNA-directed 5'-3' RNA polymerase activity / nucleotide-excision repair, DNA incision / DNA-directed RNA polymerase / transcription coregulator activity
Similarity search - Function
Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / TFIIS central domain profile. / Transcription elongation factor S-II, central domain superfamily / Transcription elongation factor S-II, central domain / TFIIS helical bundle-like domain ...Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / TFIIS central domain profile. / Transcription elongation factor S-II, central domain superfamily / Transcription elongation factor S-II, central domain / TFIIS helical bundle-like domain / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / RAD3/XPD family / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase conserved C-terminal domain / Helicase XPB/Ssl2 / Helicase XPB/Ssl2, N-terminal domain / Transcription factor Tfb2, C-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor Tfb2 / ERCC3/RAD25/XPB C-terminal helicase / ERCC3/RAD25/XPB helicase, C-terminal domain / Transcription factor TFIIH complex subunit Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / TFIIH subunit TTDA/Tfb5 / DEAD_2 / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD2 / Helicase C-terminal domain / DEXDc2 / HELICc2 / TFA2, Winged helix domain 2 / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor TFIIE, beta subunit / TFIIE beta subunit core domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIEalpha/SarR/Rpc3 HTH domain / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / TFIIE alpha subunit / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor E / Transcription factor TFE/TFIIEalpha HTH domain / TFIIF, beta subunit HTH domain / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit N-terminus / TFIIF, beta subunit, N-terminal / TFIIF beta subunit, HTH domain / TFIIS/LEDGF domain superfamily / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB, conserved site / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TATA-box binding protein, conserved site / TATA-box binding protein / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DEAH-box subfamily ATP-dependent helicases signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / TBP domain superfamily / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 7 / RNA polymerase II, heptapeptide repeat, eukaryotic / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon
Similarity search - Domain/homology
Transcription initiation factor IIB / General transcription and DNA repair factor IIH subunit TFB2 / General transcription and DNA repair factor IIH helicase subunit XPB / Transcription initiation factor IIF subunit beta / Transcription initiation factor IIF subunit alpha / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / Transcription initiation factor IIE subunit beta / Transcription initiation factor IIE subunit alpha / DNA-directed RNA polymerase II subunit RPB7 ...Transcription initiation factor IIB / General transcription and DNA repair factor IIH subunit TFB2 / General transcription and DNA repair factor IIH helicase subunit XPB / Transcription initiation factor IIF subunit beta / Transcription initiation factor IIF subunit alpha / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / Transcription initiation factor IIE subunit beta / Transcription initiation factor IIE subunit alpha / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA large subunit / DNA (> 10) / 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 RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB2 / Transcription elongation factor S-II / General transcription and DNA repair factor IIH helicase subunit XPD / DNA-directed RNA polymerase II subunit RPB1 / DNA / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsMurakami, K. / Tsai, K. / Kalisman, N. / Bushnell, D.A. / Asturias, F.J. / Kornberg, R.D.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Structure of an RNA polymerase II preinitiation complex.
Authors: Kenji Murakami / Kuang-Lei Tsai / Nir Kalisman / David A Bushnell / Francisco J Asturias / Roger D Kornberg /
Abstract: The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the ...The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription.
History
DepositionNov 3, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BQ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -1-STRANDED BARREL THIS IS REPRESENTED BY A 0-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -4-STRANDED BARREL THIS IS REPRESENTED BY A -3-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "UA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -3-STRANDED BARREL THIS IS REPRESENTED BY A -2-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3114
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: DNA REPAIR HELICASE RAD25, SSL2
2: TRANSCRIPTION ELONGATION FACTOR S-II, DST1
A: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
B: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
C: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
D: RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4
E: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1, RPB5
F: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6
G: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
H: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8
I: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
J: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10
K: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
L: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4, RPB12
M: RNA POLYMERASE II PRE-INITIATION COMPLEX, TOA1
N: NON-TEMPLATE STRAND DNA
O: TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2, TOA2
P: TRANSCRIPTION INITIATION FACTOR IIB, SUA7
Q: TATA-BOX-BINDING PROTEIN, TBP
R: TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA, TFA1
S: TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA, TFA2
T: TEMPLATE STRAND DNA
U: RNA POLYMERASE II PRE-INITIATION COMPLEX, TFG1
V: TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA, TFG2
W: RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 2, TFB2
X: RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 5, TFB5
Y: DNA REPAIR HELICASE RAD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)873,73538
Polymers873,09827
Non-polymers63711
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

+
DNA REPAIR HELICASE ... , 2 types, 2 molecules 1Y

#1: Protein DNA REPAIR HELICASE RAD25, SSL2 / GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH SUBUNIT RAD25 / TFIIH SUBUNIT RAD25 / SUPPRESSOR OF ...GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH SUBUNIT RAD25 / TFIIH SUBUNIT RAD25 / SUPPRESSOR OF STEM-LOOP MUTATION 2


Mass: 56309.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: Q00578, DNA helicase
#27: Protein DNA REPAIR HELICASE RAD3 / GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH SUBUNIT RAD3 / TFIIH SUBUNIT RAD3


Mass: 89899.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P06839, DNA helicase

+
Protein , 2 types, 2 molecules 2Q

#2: Protein TRANSCRIPTION ELONGATION FACTOR S-II, DST1 / 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


Mass: 19687.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P07273
#19: Protein TATA-BOX-BINDING PROTEIN, TBP / TATA SEQUENCE-BINDING PROTEIN / TBP / TATA-BINDING FACTOR / TATA- BOX FACTOR / TRANSCRIPTION FACTOR ...TATA SEQUENCE-BINDING PROTEIN / TBP / TATA-BINDING FACTOR / TATA- BOX FACTOR / TRANSCRIPTION FACTOR D / TRANSCRIPTION INITIATION FACTOR TFIID TBP SUBUNIT


Mass: 20120.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P13393

+
DNA-DIRECTED RNA POLYMERASE II SUBUNIT ... , 6 types, 6 molecules ABCGIK

#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / Polymerase / RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE II ...RNA POLYMERASE II SUBUNIT B1 / DNA-DIRECTED RNA POLYMERASE III LARGEST SUBUNIT / RNA POLYMERASE II SUBUNIT B220


Mass: 191821.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / Polymerase / RNA POLYMERASE II SUBUNIT 2 / B150 / DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE


Mass: 138937.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#5: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / Polymerase / RNA POLYMERASE II SUBUNIT B3 / B44.5 / DNA-DIRECTED RNA POLYMERASE II 45 KDA POLYPEPTIDE


Mass: 29921.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P16370
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / Polymerase / RNA POLYMERASE II SUBUNIT B7 / B16


Mass: 19081.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P34087
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / Polymerase / RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA- ...RNA POLYMERASE II SUBUNIT B9 / B12.6 / DNA-DIRECTED RNA POLYMERASE II 14.2 KDA POLYPEPTIDE / DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9


Mass: 13942.714 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P27999
#13: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / Polymerase / RNA POLYMERASE II SUBUNIT B11 / B13.6 / DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE


Mass: 13113.989 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P38902

+
RNA POLYMERASE II PRE-INITIATION COMPLEX, ... , 3 types, 3 molecules DMU

#6: Protein RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4


Mass: 20433.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P20433*PLUS
#15: Protein RNA POLYMERASE II PRE-INITIATION COMPLEX, TOA1


Mass: 13588.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P32773*PLUS
#23: Protein RNA POLYMERASE II PRE-INITIATION COMPLEX, TFG1


Mass: 17708.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P41895*PLUS

+
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ... , 5 types, 5 molecules EFHJL

#7: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1, RPB5 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / AND III 27 ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / AND III 27 KDA POLYPEPTIDE


Mass: 24985.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P20434
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I / AND III 23 ...RNA POLYMERASES I / II / AND III SUBUNIT ABC2 / ABC23 / DNA-DIRECTED RNA POLYMERASES I / AND III 23 KDA POLYPEPTIDE


Mass: 9675.230 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P20435
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC3 / ABC14.4 / ABC14.5 / DNA-DIRECTED RNA POLYMERASES I / AND III 14.5 KDA POLYPEPTIDE


Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P20436
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I ...RNA POLYMERASES I / II / AND III SUBUNIT ABC5 / ABC10-BETA / ABC8 / DNA-DIRECTED RNA POLYMERASES I / AND III 8.3 KDA POLYPEPTIDE


Mass: 7647.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P22139
#14: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4, RPB12 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC4 / ABC10-ALPHA


Mass: 5252.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P40422

+
DNA chain , 2 types, 2 molecules NT

#16: DNA chain NON-TEMPLATE STRAND DNA


Mass: 22483.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast)
#22: DNA chain TEMPLATE STRAND DNA


Mass: 21908.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast)

+
TRANSCRIPTION INITIATION FACTOR ... , 5 types, 5 molecules OPRSV

#17: Protein TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2, TOA2 / GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 2 / TFIIA 13.5 KDA SUBUNIT / TRANSCRIPTION INITIATION ...GENERAL TRANSCRIPTION FACTOR IIA SUBUNIT 2 / TFIIA 13.5 KDA SUBUNIT / TRANSCRIPTION INITIATION FACTOR IIA SMALL CHAIN / TRANSCRIPTION INITIATION FACTOR IIA SMALL SUBUNIT


Mass: 13473.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P32774
#18: Protein TRANSCRIPTION INITIATION FACTOR IIB, SUA7 / GENERAL TRANSCRIPTION FACTOR TFIIB / TRANSCRIPTION FACTOR E


Mass: 38257.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P29055
#20: Protein TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA, TFA1 / TFIIE-ALPHA / FACTOR A 66 KDA SUBUNIT / TRANSCRIPTION FACTOR A LARGE SUBUNIT


Mass: 18612.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P36100
#21: Protein TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA, TFA2 / TFIIE-BETA / FACTOR A 43 KDA SUBUNIT / TRANSCRIPTION FACTOR A SMALL SUBUNIT


Mass: 14524.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P36145
#24: Protein TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA, TFG2 / ATP-DEPENDENT HELICASE TFG2 / TFIIF MEDIUM SUBUNIT / TFIIF-BETA / TRANSCRIPTION FACTOR G 54 KDA SUBUNIT


Mass: 20710.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: P41896, DNA helicase

+
RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT ... , 2 types, 2 molecules WX

#25: Protein RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 2, TFB2 / GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH SUBUNIT TFB2 / TFIIH SUBUNIT TFB2 / RNA POLYMERASE ...GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH SUBUNIT TFB2 / TFIIH SUBUNIT TFB2 / RNA POLYMERASE II TRANSCRIPTION FACTOR B 52 KDA SUBUNIT / RNA POLYMERASE II TRANSCRIPTION FACTOR B P52 SUBUNIT


Mass: 7338.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: Q02939
#26: Protein RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 5, TFB5 / GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH SUBUNIT TFB5 / TFIIH SUBUNIT TFB5


Mass: 7139.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (baker's yeast) / References: UniProt: Q3E7C1

+
Non-polymers , 2 types, 11 molecules

#28: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#29: Chemical
ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: REFINED P-LOBE OF YEAST RNA POLYMERASE II PRE-INITIATION COMPLEX
Type: COMPLEX
Buffer solutionName: 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
pH: 7.6
Details: 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 14, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 22500 X / Nominal defocus max: 4000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)

-
Processing

EM softwareName: SPARX / Category: 3D reconstruction
CTF correctionDetails: SPARX
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 6 Å / Num. of particles: 7578 / Actual pixel size: 1.315 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3114. (DEPOSITION ID: 13659).
Symmetry type: POINT
RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51709 2952 11 0 54672

+
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