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- EMDB-2786: Architecture of the RNA polymerase II-Mediator core transcription... -

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Basic information

Entry
Database: EMDB / ID: EMD-2786
TitleArchitecture of the RNA polymerase II-Mediator core transcription initiation complex
Map datacITC-cMed
Sample
  • Sample: cITC-cMed
  • Protein or peptide: x 31 types
  • DNA: x 2 types
  • RNA: x 1 types
Keywordstranscription / transcription initiation / RNA polymerase II / General Transcription Factors / Mediator
Function / homology
Function and homology information


meiotic gene conversion / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / TFIIH-class transcription factor complex binding / core mediator complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding ...meiotic gene conversion / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / TFIIH-class transcription factor complex binding / core mediator complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / mediator complex / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / transcription factor TFIIA complex / : / RNA polymerase I preinitiation complex assembly / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / DNA binding, bending / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / termination of RNA polymerase II transcription / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA polymerase II general transcription initiation factor activity / 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 / transcription factor TFIID complex / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / 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 / transcription elongation by RNA polymerase I / TFIID-class transcription factor complex binding / positive regulation of translational initiation / RNA polymerase II activity / TFIIB-class transcription factor binding / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / translesion synthesis / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / peroxisome / cytoplasmic stress granule / transcription corepressor activity / disordered domain specific binding / protein-macromolecule adaptor activity / single-stranded DNA binding / ribosome biogenesis / DNA-binding transcription factor binding / DNA recombination / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / single-stranded RNA binding / nucleic acid binding / transcription coactivator activity / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Mediator complex, subunit Med19, fungi / Rox3 mediator complex subunit / Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 ...Mediator complex, subunit Med19, fungi / Rox3 mediator complex subunit / Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med7 superfmaily / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / 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. / Transcription factor TFIIB / Zinc finger TFIIB-type profile. / Zinc finger, TFIIB-type / TFIIB zinc-binding / 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-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase RBP11 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Zinc finger TFIIS-type signature. / Cyclin-like superfamily / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase, Rpb8
Similarity search - Domain/homology
Transcription initiation factor IIF subunit alpha / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB3 / Mediator of RNA polymerase II transcription subunit 14 / 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 ...Transcription initiation factor IIF subunit alpha / DNA-directed RNA polymerase II subunit RPB1 / DNA-directed RNA polymerase II subunit RPB2 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB3 / Mediator of RNA polymerase II transcription subunit 14 / 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 / Mediator of RNA polymerase II transcription subunit 19 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 9 / DNA-directed RNA polymerase II subunit RPB7 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 6 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit beta / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces mikatae (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsPlaschka C / Lariviere L / Wenzeck L / Hemann M / Tegunov D / Petrotchenko EV / Borchers CH / Baumeister W / Herzog F / Villa E / Cramer P
CitationJournal: Nature / Year: 2015
Title: Architecture of the RNA polymerase II-Mediator core initiation complex.
Authors: C Plaschka / L Larivière / L Wenzeck / M Seizl / M Hemann / D Tegunov / E V Petrotchenko / C H Borchers / W Baumeister / F Herzog / E Villa / P Cramer /
Abstract: The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all ...The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.
History
DepositionSep 21, 2014-
Header (metadata) releaseOct 29, 2014-
Map releaseFeb 4, 2015-
UpdateMar 4, 2015-
Current statusMar 4, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v1o
  • Surface level: 0.0135
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2786.png

Downloads & links

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Map

FileDownload / File: emd_2786.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcITC-cMed
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.0135 / Movie #1: 0.0135
Minimum - Maximum-0.02174095 - 0.05509891
Average (Standard dev.)0.00042752 (±0.00378394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0220.0550.000

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Supplemental data

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Sample components

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Entire : cITC-cMed

EntireName: cITC-cMed
Components
  • Sample: cITC-cMed
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4RNA polymerase
  • Protein or peptide: TRANSCRIPTION INITIATION FACTOR IIB
  • Protein or peptide: TATA-box-binding protein
  • Protein or peptide: Transcription initiation factor IIF subunit alpha
  • Protein or peptide: Transcription initiation factor IIF subunit beta
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 4
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 6
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 7
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 8
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 9
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 10
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 11
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 14
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 17
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 18
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 19
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 20
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 21
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 22
  • Protein or peptide: Mediator of RNA polymerase II transcription subunit 31
  • DNA: template DNA
  • DNA: nontemplate DNA
  • RNA: RNA

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Supramolecule #1000: cITC-cMed

SupramoleculeName: cITC-cMed / type: sample / ID: 1000 / Number unique components: 34
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / type: protein_or_peptide / ID: 1 / Name.synonym: RPO21 RPB1 RPB220 SUA8 YDL140C D2150 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 192 KDa / Theoretical: 192 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB1

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Macromolecule #2: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / type: protein_or_peptide / ID: 2 / Name.synonym: RPB2 RPB150 RPO22 YOR151C / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 139 KDa / Theoretical: 139 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB2

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Macromolecule #3: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / type: protein_or_peptide / ID: 3 / Name.synonym: RPB3 YIL021W / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 35 KDa / Theoretical: 35 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB3

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Macromolecule #4: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / type: protein_or_peptide / ID: 4 / Name.synonym: RPB4 YJL140W J0654 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB4

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Macromolecule #5: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
type: protein_or_peptide / ID: 5 / Name.synonym: RPB5 RPA7 RPC9 YBR154C YBR1204 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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Macromolecule #6: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
type: protein_or_peptide / ID: 6 / Name.synonym: RPO26 RPB6 YPR187W P9677.8 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 18 KDa / Theoretical: 18 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #7: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / type: protein_or_peptide / ID: 7 / Name.synonym: RPB7 YDR404C D9509.22 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 19 KDa / Theoretical: 19 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB7

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Macromolecule #8: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
type: protein_or_peptide / ID: 8 / Name.synonym: RPB8 YOR224C YOR50-14 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 17 KDa / Theoretical: 17 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

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Macromolecule #9: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / type: protein_or_peptide / ID: 9 / Name.synonym: RPB9 YGL070C / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 14 KDa / Theoretical: 14 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #10: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
type: protein_or_peptide / ID: 10 / Name.synonym: RPB10 YOR210W / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 8 KDa / Theoretical: 8 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

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Macromolecule #11: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / type: protein_or_peptide / ID: 11 / Name.synonym: RPB11 YOL005C / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 13 KDa / Theoretical: 13 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB11

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Macromolecule #12: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
type: protein_or_peptide / ID: 12 / Name.synonym: RPC10 RPB12 YHR143W-A YHR143BW / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 8 KDa / Theoretical: 8 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

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Macromolecule #13: TRANSCRIPTION INITIATION FACTOR IIB

MacromoleculeName: TRANSCRIPTION INITIATION FACTOR IIB / type: protein_or_peptide / ID: 13 / Name.synonym: SUA7 YPR086W P9513.4 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 38 KDa / Theoretical: 38 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Transcription initiation factor IIB

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Macromolecule #14: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 14 / Name.synonym: SPT15, BTF1, TBP1, YER148W / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 20 KDa / Theoretical: 20 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: TATA-box-binding protein

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Macromolecule #15: Transcription initiation factor IIF subunit alpha

MacromoleculeName: Transcription initiation factor IIF subunit alpha / type: protein_or_peptide / ID: 15 / Name.synonym: Tfg1 SSU71 RAP74 YGR186W / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces mikatae (yeast)
Molecular weightExperimental: 82 KDa / Theoretical: 82 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Transcription initiation factor IIB

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Macromolecule #16: Transcription initiation factor IIF subunit beta

MacromoleculeName: Transcription initiation factor IIF subunit beta / type: protein_or_peptide / ID: 16 / Name.synonym: TFG2, YGR005C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 47 KDa / Theoretical: 47 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Transcription initiation factor IIF subunit beta

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Macromolecule #17: Mediator of RNA polymerase II transcription subunit 4

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 4 / type: protein_or_peptide / ID: 17 / Name.synonym: MED4, YOR174W, O3630 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 32 KDa / Theoretical: 32 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 4

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Macromolecule #18: Mediator of RNA polymerase II transcription subunit 6

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 6 / type: protein_or_peptide / ID: 18 / Name.synonym: MED6, MTR32, YHR058C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 33 KDa / Theoretical: 33 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 6

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Macromolecule #19: Mediator of RNA polymerase II transcription subunit 7

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 7 / type: protein_or_peptide / ID: 19 / Name.synonym: MED7, YOL135C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 26 KDa / Theoretical: 26 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 7

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Macromolecule #20: Mediator of RNA polymerase II transcription subunit 8

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 8 / type: protein_or_peptide / ID: 20 / Name.synonym: MED8, YBR193C, YBR1403 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 8

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Macromolecule #21: Mediator of RNA polymerase II transcription subunit 9

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 9 / type: protein_or_peptide / ID: 21 / Name.synonym: CSE2, MED9, YNR010W, N2046 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 17 KDa / Theoretical: 17 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 9

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Macromolecule #22: Mediator of RNA polymerase II transcription subunit 10

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 10
type: protein_or_peptide / ID: 22 / Name.synonym: NUT2, MED10, YPR168W, P9325.2 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 18 KDa / Theoretical: 18 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 10

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Macromolecule #23: Mediator of RNA polymerase II transcription subunit 11

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 11
type: protein_or_peptide / ID: 23 / Name.synonym: MED11, YMR112C, YM9718.11C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 13 KDa / Theoretical: 13 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 11

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Macromolecule #24: Mediator of RNA polymerase II transcription subunit 14

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 14
type: protein_or_peptide / ID: 24 / Name.synonym: RGR1, MED14, YLR071C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 85 KDa / Theoretical: 85 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 14

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Macromolecule #25: Mediator of RNA polymerase II transcription subunit 17

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 17
type: protein_or_peptide / ID: 25 / Name.synonym: SRB4, MED17, YER022W / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 79 KDa / Theoretical: 79 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 17

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Macromolecule #26: Mediator of RNA polymerase II transcription subunit 18

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 18
type: protein_or_peptide / ID: 26 / Name.synonym: SRB5, MED18, YGR104C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 34 KDa / Theoretical: 34 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 18

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Macromolecule #27: Mediator of RNA polymerase II transcription subunit 19

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 19
type: protein_or_peptide / ID: 27 / Name.synonym: ROX3, MED19, NUT3, SSN7, YBL093C, YBL0837 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 19

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Macromolecule #28: Mediator of RNA polymerase II transcription subunit 20

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 20
type: protein_or_peptide / ID: 28 / Name.synonym: SRB2, HRS2, MED20, YHR041C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 23 KDa / Theoretical: 23 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 20

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Macromolecule #29: Mediator of RNA polymerase II transcription subunit 21

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 21
type: protein_or_peptide / ID: 29 / Name.synonym: SRB7, MED21, YDR308C, D9740.17 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 16 KDa / Theoretical: 16 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 21

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Macromolecule #30: Mediator of RNA polymerase II transcription subunit 22

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 22
type: protein_or_peptide / ID: 30 / Name.synonym: SRB6, MED22, YBR253W, YBR1721 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 14 KDa / Theoretical: 14 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 22

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Macromolecule #31: Mediator of RNA polymerase II transcription subunit 31

MacromoleculeName: Mediator of RNA polymerase II transcription subunit 31
type: protein_or_peptide / ID: 31 / Name.synonym: SOH1, MED31, YGL127C, G2864 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 15 KDa / Theoretical: 15 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Mediator of RNA polymerase II transcription subunit 31

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Macromolecule #32: template DNA

MacromoleculeName: template DNA / type: dna / ID: 32 / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
SequenceString:
CGAGAACAGT AGCACGCTGT GTATATAATA GTGTGTTGTA CATAGCGGAG GTCGGTGGGG CACAACTGCG CT

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Macromolecule #33: nontemplate DNA

MacromoleculeName: nontemplate DNA / type: dna / ID: 33 / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
SequenceString:
AGCGCAGTTG TGCTATGATA TTTTTATGTA TGTACAACAC ACTATTATAT ACACAGCGTG CTACTGTTCT CG

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Macromolecule #34: RNA

MacromoleculeName: RNA / type: rna / ID: 34 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
SequenceString:
AUAUCA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.5
Details: 25 mM HEPES-KOH pH 7.5, 180 mM Potassium acetate, 5 % Glycerol, 5 mM DTT
VitrificationCryogen name: ETHANE / Instrument: OTHER
Method: Grids were glow-discharged for 20 s before deposition of 4 microliters sample and incubated for 30 s. Grids were washed twice with 4 microliters distilled water, blotted, and then vitrified.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 2972 / Average electron dose: 25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: OTHER / Software - Name: RELION, 1.2
Details: The density was filtered according to local resolution and further a temperature factor of minus 340 A2 was applied.
Number images used: 3267
DetailsParticles were picked using EMAN2 and were processed using RELION 1.2.

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