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- PDB-5fmf: the P-lobe of RNA polymerase II pre-initiation complex -

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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 ...) x 6
  • (DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT ...) 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 mitotic recombination / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / RNA polymerase II promoter clearance / transcription factor TFIIIB complex / positive regulation of mitotic recombination ...regulation of mitotic recombination / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / regulation of mRNA 3'-end processing / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / RNA polymerase II promoter clearance / transcription factor TFIIIB complex / positive regulation of mitotic recombination / RNA polymerase I general transcription initiation factor binding / transcription factor TFIIE complex / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / regulation of transcription by RNA polymerase III / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / transcription factor TFIIF complex / DNA 5'-3' helicase / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / DNA binding, bending / RNA Polymerase I Transcription Initiation / transcription preinitiation complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / DNA 3'-5' helicase / 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 / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / transcription factor TFIID complex / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / 3'-5' DNA helicase activity / 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 / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / RNA polymerase II complex binding / ATPase activator activity / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / positive regulation of translational initiation / Dual incision in TC-NER / protein phosphatase activator activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / ATP-dependent activity, acting on DNA / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase II preinitiation complex assembly / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / DNA helicase activity / TBP-class protein binding / transcription coregulator activity / transcription antitermination / nucleotide-excision repair / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / disordered domain specific binding / DNA-directed RNA polymerase activity / peroxisome / ribosome biogenesis / single-stranded DNA binding
Similarity search - Function
: / Tfa2 E-tether / Bacterial type XPD DNA helicase, FeS cluster domain / 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. ...: / Tfa2 E-tether / Bacterial type XPD DNA helicase, FeS cluster domain / 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 / RAD3/XPD family / Helicase XPB/Ssl2 / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Helical and beta-bridge domain / Helical and beta-bridge domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIH subunit TTDA/Tfb5 / Transcription initiation factor TFIIE, beta subunit / TFB5-like superfamily / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / Transcription factor TFIIH complex subunit Tfb5 / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription factor TFIIH complex subunit Tfb5 / ATP-dependent helicase Rad3/Chl1-like / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / TFIIB zinc-binding / TFIIS/LEDGF domain superfamily / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / 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 / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / 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 / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIE subunit alpha / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta / General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 / General transcription and DNA repair factor IIH subunit TFB2 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer'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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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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
Water00
1


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

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Components

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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 (brewer'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 (brewer's yeast) / References: UniProt: P06839, DNA helicase

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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 (brewer'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 (brewer's yeast) / References: UniProt: P13393

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

#3: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / 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 (brewer's yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#4: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / 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 (brewer's yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#5: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / 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 (brewer's yeast) / References: UniProt: P16370
#9: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / 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 (brewer's yeast) / References: UniProt: P34087
#11: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / 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 (brewer's yeast) / References: UniProt: P27999
#13: Protein DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / 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 (brewer's yeast) / References: UniProt: P38902

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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 (brewer'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 (brewer'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 (brewer's yeast) / References: UniProt: P41895*PLUS

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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 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 (brewer's yeast) / References: UniProt: P20434
#8: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6 / 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 (brewer's yeast) / References: UniProt: P20435
#10: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8 / 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 (brewer's yeast) / References: UniProt: P20436
#12: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10 / 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 (brewer's yeast) / References: UniProt: P22139
#14: Protein/peptide DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4, RPB12 / 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 (brewer's yeast) / References: UniProt: P40422

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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 (brewer'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 (brewer's yeast)

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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 (brewer'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 (brewer'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 (brewer'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 (brewer'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 (brewer's yeast) / References: UniProt: P41896, DNA helicase

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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 (brewer'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 (brewer's yeast) / References: UniProt: Q3E7C1

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Non-polymers , 2 types, 11 molecules

#28: Chemical ChemComp-MG / MAGNESIUM ION


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


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

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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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,

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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 FIELD / 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)

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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

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