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- EMDB-3846: STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH -

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Basic information

Entry
Database: EMDB / ID: EMD-3846
TitleSTRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH
Map data
SamplePre-Initiation Complex (PIC)
  • Polymerase
  • initiation factorsInitiation factor
  • (Transcription ...) x 8
  • nucleic acid
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (nucleic-acidNucleic acid) x 2
  • TATA-box-binding protein
  • (DNA repair helicase ...) x 2
  • (RNA polymerase II transcription factor B subunit ...) x 5
  • Suppressor of stem-loop protein 1
  • Unknown protein
  • (ligand) x 3
Function / homology
Function and homology information


Cyclin E associated events during G1/S transition / regulation of transposition, RNA-mediated / regulation of mitotic recombination / 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 TFIIK complex / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex ...Cyclin E associated events during G1/S transition / regulation of transposition, RNA-mediated / regulation of mitotic recombination / 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 TFIIK complex / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / positive regulation of mitotic recombination / RNA polymerase III transcription regulatory region sequence-specific DNA binding / phosphatidylinositol-5-phosphate 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 / cyclin-dependent protein serine/threonine kinase activator activity / 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 / phosphatidylinositol-3-phosphate binding / 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 Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / 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 / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / response to UV / translation initiation factor binding / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription elongation from RNA polymerase II promoter / TBP-class protein binding / nucleotide-excision repair / 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
Similarity search - Function
Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Transcription factor Tfb4 / TFIIH subunit Tfb4/GTF2H3 / TFIIH subunit Tfb1/GTF2H1 / RAD3/XPD family / TFIIH p62 subunit, N-terminal domain / TFIIH C1-like domain ...Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Transcription factor Tfb4 / TFIIH subunit Tfb4/GTF2H3 / TFIIH subunit Tfb1/GTF2H1 / RAD3/XPD family / TFIIH p62 subunit, N-terminal domain / TFIIH C1-like domain / TFIIH subunit Ssl1/p44 / TFIIH p62 subunit, N-terminal / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / Ssl1-like / BSD domain / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase conserved C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helicase XPB/Ssl2 / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / ERCC3/RAD25/XPB C-terminal helicase / ERCC3/RAD25/XPB helicase, C-terminal domain / TFB5-like superfamily / TFIIH subunit TTDA/Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / DEAD2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEAD_2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / ATP-dependent helicase, C-terminal / HELICc2 / DEXDc2 / Helicase-like, DEXD box c2 type / TFA2, Winged helix domain 2 / Transcription initiation factor TFIIE, beta subunit / TFA2 Winged helix domain 2 / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIE beta subunit core domain / TFIIE beta central core DNA-binding domain profile. / Transcription factor E / Transcription initiation factor IIE subunit alpha, N-terminal / TFIIE alpha subunit / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / TFIIF beta subunit, HTH domain / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / TFIIF, beta subunit, N-terminal / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription initiation factor IIF, alpha subunit / 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 initiation factor IIA, gamma subunit, C-terminal / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB repeat / Transcription factor TFIIB, conserved site / Transcription factor TFIIB, cyclin-like domain / 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 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 6 / RNA polymerase II, heptapeptide repeat, eukaryotic
Similarity search - Domain/homology
General transcription and DNA repair factor IIH subunit TFB1 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH subunit SSL1 / RNA polymerase II transcription factor B subunit 3 / 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 ...General transcription and DNA repair factor IIH subunit TFB1 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH subunit SSL1 / RNA polymerase II transcription factor B subunit 3 / 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 / DNA-directed RNA polymerase II subunit RPB4 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA large subunit / Transcription initiation factor IIB / 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 RPB3 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB2 / General transcription and DNA repair factor IIH helicase subunit XPD / DNA-directed RNA polymerase II subunit RPB1 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsSchilbach S / Hantsche M / Tegunov D / Dienemann C / Wigge C / Urlaub H / Cramer P
CitationJournal: Nature / Year: 2017
Title: Structures of transcription pre-initiation complex with TFIIH and Mediator.
Authors: S Schilbach / M Hantsche / D Tegunov / C Dienemann / C Wigge / H Urlaub / P Cramer /
Abstract: For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron ...For the initiation of transcription, RNA polymerase II (Pol II) assembles with general transcription factors on promoter DNA to form the pre-initiation complex (PIC). Here we report cryo-electron microscopy structures of the Saccharomyces cerevisiae PIC and PIC-core Mediator complex at nominal resolutions of 4.7 Å and 5.8 Å, respectively. The structures reveal transcription factor IIH (TFIIH), and suggest how the core and kinase TFIIH modules function in the opening of promoter DNA and the phosphorylation of Pol II, respectively. The TFIIH core subunit Ssl2 (a homologue of human XPB) is positioned on downstream DNA by the 'E-bridge' helix in TFIIE, consistent with TFIIE-stimulated DNA opening. The TFIIH kinase module subunit Tfb3 (MAT1 in human) anchors the kinase Kin28 (CDK7), which is mobile in the PIC but preferentially located between the Mediator hook and shoulder in the PIC-core Mediator complex. Open spaces between the Mediator head and middle modules may allow access of the kinase to its substrate, the C-terminal domain of Pol II.
History
DepositionAug 11, 2017-
Header (metadata) releaseApr 25, 2018-
Map releaseApr 25, 2018-
UpdateApr 25, 2018-
Current statusApr 25, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5oqj
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3846.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 350 pix.
= 479.5 Å
1.37 Å/pix.
x 350 pix.
= 479.5 Å
1.37 Å/pix.
x 350 pix.
= 479.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.066 / Movie #1: 0.066
Minimum - Maximum-0.20505115 - 0.5921751
Average (Standard dev.)0.0014869234 (±0.0113299545)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 479.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z479.500479.500479.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.2050.5920.001

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Supplemental data

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Sample components

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Entire Pre-Initiation Complex (PIC)

EntireName: Pre-Initiation Complex (PIC) / Details: PRE-INITIATION COMPLEX WITH TFIIH / Number of Components: 39

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Component #1: protein, Pre-Initiation Complex (PIC)

ProteinName: Pre-Initiation Complex (PIC) / Details: PRE-INITIATION COMPLEX WITH TFIIH / Recombinant expression: No
MassTheoretical: 1.43 MDa

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Component #2: protein, Polymerase

ProteinName: Polymerase / Details: natural source entities / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #3: protein, initiation factors

ProteinName: initiation factorsInitiation factor / Details: entitites expressed in coli / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #4: protein, Transcription factors

ProteinName: Transcription factorsTranscription factor / Details: entitites expressed in T.ni / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #5: protein, nucleic acid

ProteinName: nucleic acid / Details: Synthetic nucleic acid / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #6: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 191.821578 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, DNA-directed RNA polymerase II subunit RPB2

ProteinName: DNA-directed RNA polymerase II subunit RPB2Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 138.937297 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.330457 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, DNA-directed RNA polymerase II subunit RPB4

ProteinName: DNA-directed RNA polymerase II subunit RPB4Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.451191 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.117094 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.931834 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.081053 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.525363 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.308161 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.290732 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, DNA-directed RNA polymerase II subunit RPB11

ProteinName: DNA-directed RNA polymerase II subunit RPB11Polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.633493 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.729969 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, Transcription initiation factor IIB

ProteinName: Transcription initiation factor IIB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.25734 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #19: nucleic-acid, NONTEMPLATE DNA

nucleic acidName: NONTEMPLATE DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DG)(DA)(DG)(DA)(DA)(DC)(DA)(DG)(DT) (DA)(DG)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DA)(DT)(DA) (DG)(DC)(DT)(DA)(DT)(DG)(DG)(DA)(DA)(DC) (DG)(DT)(DT)(DC)(DG)(DA) ...Sequence:
(DC)(DG)(DA)(DG)(DA)(DA)(DC)(DA)(DG)(DT) (DA)(DG)(DC)(DA)(DC)(DG)(DC)(DT)(DG)(DT) (DG)(DT)(DA)(DT)(DA)(DT)(DA)(DA)(DT)(DA) (DG)(DC)(DT)(DA)(DT)(DG)(DG)(DA)(DA)(DC) (DG)(DT)(DT)(DC)(DG)(DA)(DT)(DT)(DC)(DA) (DC)(DC)(DT)(DC)(DC)(DG)(DA)(DT)(DG)(DT) (DG)(DT)(DG)(DT)(DT)(DG)(DT)(DA)(DC)(DA) (DT)(DA)(DC)(DA)(DT)(DA)(DA)(DA)(DA)(DA) (DT)(DA)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DA) (DC)(DA)(DA)(DC)(DT)(DG)(DC)(DG)(DC)(DT) (DG)(DT)(DG)(DT)(DC)(DA)
MassTheoretical: 32.716977 kDa
SourceSpecies: synthetic construct (others)

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Component #20: protein, TATA-box-binding protein

ProteinName: TATA-box-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.042275 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #21: protein, Transcription initiation factor IIF subunit alpha

ProteinName: Transcription initiation factor IIF subunit alpha / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 82.32057 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #22: protein, Transcription initiation factor IIF subunit beta

ProteinName: Transcription initiation factor IIF subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.684492 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #23: nucleic-acid, TEMPLATE DNA

nucleic acidName: TEMPLATE DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DG)(DA)(DC)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DA)(DG)(DT)(DT)(DG)(DT)(DG)(DC)(DT) (DA)(DT)(DG)(DA)(DT)(DA)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DG)(DT)(DA)(DT)(DG)(DT)(DA) (DC)(DA)(DA)(DC)(DA)(DC) ...Sequence:
(DT)(DG)(DA)(DC)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DA)(DG)(DT)(DT)(DG)(DT)(DG)(DC)(DT) (DA)(DT)(DG)(DA)(DT)(DA)(DT)(DT)(DT)(DT) (DT)(DA)(DT)(DG)(DT)(DA)(DT)(DG)(DT)(DA) (DC)(DA)(DA)(DC)(DA)(DC)(DA)(DC)(DA)(DT) (DC)(DG)(DG)(DA)(DG)(DG)(DT)(DG)(DA)(DA) (DT)(DC)(DG)(DA)(DA)(DC)(DG)(DT)(DT)(DC) (DC)(DA)(DT)(DA)(DG)(DC)(DT)(DA)(DT)(DT) (DA)(DT)(DA)(DT)(DA)(DC)(DA)(DC)(DA)(DG) (DC)(DG)(DT)(DG)(DC)(DT)(DA)(DC)(DT)(DG) (DT)(DT)(DC)(DT)(DC)(DG)
MassTheoretical: 32.68092 kDa
SourceSpecies: synthetic construct (others)

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Component #24: protein, Transcription initiation factor IIA large subunit

ProteinName: Transcription initiation factor IIA large subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.230805 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #25: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.47307 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #26: protein, Transcription initiation factor IIE subunit alpha

ProteinName: Transcription initiation factor IIE subunit alpha / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.538461 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #27: protein, Transcription initiation factor IIE subunit beta

ProteinName: Transcription initiation factor IIE subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.050434 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli BL21(DE3) (bacteria)

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Component #28: protein, DNA repair helicase RAD3

ProteinName: DNA repair helicase RAD3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 89.064555 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #29: protein, RNA polymerase II transcription factor B subunit 1

ProteinName: RNA polymerase II transcription factor B subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 65.440922 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #30: protein, RNA polymerase II transcription factor B subunit 2

ProteinName: RNA polymerase II transcription factor B subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.406277 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #31: protein, RNA polymerase II transcription factor B subunit 3

ProteinName: RNA polymerase II transcription factor B subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.188438 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #32: protein, RNA polymerase II transcription factor B subunit 4

ProteinName: RNA polymerase II transcription factor B subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.403598 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #33: protein, RNA polymerase II transcription factor B subunit 5

ProteinName: RNA polymerase II transcription factor B subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.24349 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #34: protein, Suppressor of stem-loop protein 1

ProteinName: Suppressor of stem-loop protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.122695 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #35: protein, DNA repair helicase RAD25

ProteinName: DNA repair helicase RAD25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.049695 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #36: protein, Unknown protein

ProteinName: Unknown protein
Details: Residues indicated as UNK with the chain identifier Z are part of an assembly between the clutch domains of Tfb2 and Ssl2 but could not be assigned to any of the two proteins with confidence ...Details: Residues indicated as UNK with the chain identifier Z are part of an assembly between the clutch domains of Tfb2 and Ssl2 but could not be assigned to any of the two proteins with confidence since domain swapping/beta-strand exchange may occur. To account for this uncertainty, a theoretical chain Z was introduced for this residue range but not assigned to any of the PIC components.
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.677524 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #37: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #38: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #39: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.7 mg/mL / pH: 7.6
Support filmQUANTIFOIL HOLEY GOLD GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF SAMPLE.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE
Details: GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 42 e/Å2 / Illumination Mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 500.0 - 5000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of Digital Images: 13000

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 58000
3D reconstructionResolution: 4.7 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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