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- EMDB-0091: Structure of a yeast closed complex with distorted DNA (core CCdist) -

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Basic information

Entry
Database: EMDB / ID: EMD-0091
TitleStructure of a yeast closed complex with distorted DNA (core CCdist)
Map data
SamplePre-initiation complexPreinitiation complex
  • Polymerase
  • TIFs
  • nucleic acidsNucleic acid
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • Transcription initiation factor IIB
  • (nucleic-acidNucleic acid) x 2
  • TATA-box-binding protein
  • (Transcription initiation factor IIF subunit ...) x 2
  • (Transcription initiation factor IIA ...) x 2
  • (Transcription initiation factor IIE subunit ...) x 2
  • (ligand) x 2
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / promoter clearance from RNA polymerase II promoter / TFIIA-class transcription factor complex binding / dephosphorylation of RNA polymerase II C-terminal domain / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIE complex / TFIIF-class transcription factor complex binding / RNA polymerase I general transcription initiation factor binding ...RNA polymerase II complex recruiting activity / promoter clearance from RNA polymerase II promoter / TFIIA-class transcription factor complex binding / dephosphorylation of RNA polymerase II C-terminal domain / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / transcription factor TFIIE complex / TFIIF-class transcription factor complex binding / RNA polymerase I general transcription initiation factor binding / regulation of protein serine/threonine phosphatase activity / transcription factor TFIIF complex / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / transposon integration / nucleolar large rRNA transcription by RNA polymerase I / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / general transcription initiation factor activity / RNA polymerase I preinitiation complex assembly / nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / RNA polymerase II preinitiation complex assembly / positive regulation of transcription regulatory region DNA binding / DNA binding, bending / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / RNA polymerase II transcribes snRNA genes / mRNA Capping / transcription factor TFIID complex / RNA Polymerase I Promoter Escape / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / RNA polymerase II activity / RNA polymerase II complex binding / RNA polymerase I activity / protein phosphatase activator activity / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / positive regulation of translational initiation / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / tRNA transcription by RNA polymerase III / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / transcription by RNA polymerase I / transcription-coupled nucleotide-excision repair / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / translesion synthesis / transcription preinitiation complex / RNA polymerase II, core complex / RNA polymerase II core promoter sequence-specific DNA binding / transcription elongation from RNA polymerase II promoter / transcription initiation from RNA polymerase II promoter / translation initiation factor binding / TBP-class protein binding / positive regulation of transcription elongation from RNA polymerase II promoter / P-body / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / transcription coregulator activity / transcription, RNA-templated / cytoplasmic stress granule / single-stranded DNA binding / DNA-binding transcription factor binding / ribosome biogenesis / disordered domain specific binding / single-stranded RNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / protein dimerization activity / mRNA binding / nucleotide binding / chromatin binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / metal ion binding
Similarity search - Function
TFIIE beta subunit core domain / TFA2, Winged helix domain 2 / TFA2 Winged helix domain 2 / Transcription initiation factor TFIIE, beta subunit / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIE beta central core DNA-binding domain profile. / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFE/IIEalpha-type HTH domain profile. ...TFIIE beta subunit core domain / TFA2, Winged helix domain 2 / TFA2 Winged helix domain 2 / Transcription initiation factor TFIIE, beta subunit / Transcription factor TFIIE beta subunit, DNA-binding domain / TFIIE beta central core DNA-binding domain profile. / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFE/IIEalpha-type HTH domain profile. / Transcription factor E / TFIIE alpha subunit / Transcription initiation factor IIE / TFIIF, beta subunit, N-terminal / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / TFIIF beta subunit, HTH domain / 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 initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB repeat / Transcription factor TFIIB, conserved site / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / TATA-box binding protein, conserved site / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TBP domain superfamily / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like / Cyclin-like superfamily / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerases N / 8 Kd subunits signature. / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / 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 Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / RNA polymerase, Rpb5, N-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase, Rpb8 / RNA polymerase subunit 8 / RNA polymerase Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerases H / 23 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature.
Similarity search - Domain/homology
Transcription initiation factor IIB / Transcription initiation factor IIF subunit alpha / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / Transcription initiation factor IIE subunit beta / Transcription initiation factor IIE subunit alpha / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA large subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC3 ...Transcription initiation factor IIB / Transcription initiation factor IIF subunit alpha / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / Transcription initiation factor IIE subunit beta / Transcription initiation factor IIE subunit alpha / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA large subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / 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 RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerase II subunit RPB3 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / Transcription initiation factor IIF subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsDienemann C / Schwalb B / Schilbach S / Cramer P
Funding support Germany, 2 items
OrganizationGrant numberCountry
European Research Council693023 Germany
German Research FoundationSFB860 Germany
CitationJournal: Mol Cell / Year: 2019
Title: Promoter Distortion and Opening in the RNA Polymerase II Cleft.
Authors: Christian Dienemann / Björn Schwalb / Sandra Schilbach / Patrick Cramer /
Abstract: Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron ...Transcription initiation requires opening of promoter DNA in the RNA polymerase II (Pol II) pre-initiation complex (PIC), but it remains unclear how this is achieved. Here we report the cryo-electron microscopic (cryo-EM) structure of a yeast PIC that contains underwound, distorted promoter DNA in the closed Pol II cleft. The DNA duplex axis is offset at the upstream edge of the initially melted DNA region (IMR) where DNA opening begins. Unstable IMRs are found in a subset of yeast promoters that we show can still initiate transcription after depletion of the transcription factor (TF) IIH (TFIIH) translocase Ssl2 (XPB in human) from the nucleus in vivo. PIC-induced DNA distortions may thus prime the IMR for melting and may explain how unstable IMRs that are predicted in promoters of Pol I and Pol III can open spontaneously. These results suggest that DNA distortion in the polymerase cleft is a general mechanism that contributes to promoter opening.
History
DepositionJun 30, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseDec 5, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0028
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6gyl
  • Surface level: 0.0028
  • 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_0091.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 300 pix.
= 315. Å
1.05 Å/pix.
x 300 pix.
= 315. Å
1.05 Å/pix.
x 300 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.0028 / Movie #1: 0.0028
Minimum - Maximum-0.010854901 - 0.021589203
Average (Standard dev.)-0.00002990702 (±0.0007890197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z315.000315.000315.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0110.022-0.000

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Supplemental data

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Additional map: Relion post-processed map (Bfactor -100) masked (threshold 0.0042,...

Fileemd_0091_additional.map
AnnotationRelion post-processed map (Bfactor -100) masked (threshold 0.0042, 3px hard, 10 px soft)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1

Fileemd_0091_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_0091_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Pre-initiation complex

EntireName: Pre-initiation complexPreinitiation complex / Number of Components: 28

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Component #1: protein, Pre-initiation complex

ProteinName: Pre-initiation complexPreinitiation complex / Recombinant expression: No

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Component #2: protein, Polymerase

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

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Component #3: protein, TIFs

ProteinName: TIFs / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, nucleic acids

ProteinName: nucleic acidsNucleic acid / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: synthetic construct (others)

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Component #5: 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 #6: 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 #7: 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 #8: 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 #9: 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 #10: 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 #11: 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 #12: 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 #13: 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 #14: 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 #15: 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 #16: 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 #17: 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 (E. coli)

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Component #18: nucleic-acid, GAT1 promoter DNA

nucleic acidName: GAT1 promoter DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DG)(DC)(DC)(DC)(DG)(DG)(DC)(DC)(DC) (DA)(DG)(DC)(DC)(DA)(DC)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DG)(DG)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DC)(DA)(DC)(DT)(DC)(DC) (DC)(DG)(DG)(DC)(DC)(DC) ...Sequence:
(DT)(DG)(DC)(DC)(DC)(DG)(DG)(DC)(DC)(DC) (DA)(DG)(DC)(DC)(DA)(DC)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DG)(DG)(DT)(DG)(DT) (DG)(DT)(DG)(DC)(DC)(DA)(DC)(DT)(DC)(DC) (DC)(DG)(DG)(DC)(DC)(DC)(DC)(DG)(DG)(DT) (DA)(DT)(DT)(DA)(DG)(DC)
MassTheoretical: 17.129941 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #19: 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 (E. coli)

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Component #20: 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 (E. coli)

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Component #21: 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 (E. coli)

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Component #22: nucleic-acid, GAT1 promoter DNA

nucleic acidName: GAT1 promoter DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DG)(DC)(DT)(DA)(DA)(DT)(DA)(DC)(DC)(DG) (DG)(DG)(DG)(DC)(DC)(DG)(DG)(DG)(DA)(DG) (DT)(DG)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DC) (DC)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DG)(DT)(DG)(DG)(DC)(DT) ...Sequence:
(DG)(DC)(DT)(DA)(DA)(DT)(DA)(DC)(DC)(DG) (DG)(DG)(DG)(DC)(DC)(DG)(DG)(DG)(DA)(DG) (DT)(DG)(DG)(DC)(DA)(DC)(DA)(DC)(DA)(DC) (DC)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DG)(DT)(DG)(DG)(DC)(DT)(DG)(DG)(DG)(DC) (DC)(DG)(DG)(DG)(DC)(DA)
MassTheoretical: 17.388111 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Component #23: protein, Transcription initiation factor IIA large subunit,Transc...

ProteinName: Transcription initiation factor IIA large subunit,Transcription initiation factor IIA large subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.432029 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #24: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.431131 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #25: protein, Transcription initiation factor IIE subunit alpha,Tfa1,Tfa1

ProteinName: Transcription initiation factor IIE subunit alpha,Tfa1,Tfa1
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 (E. coli)

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Component #26: 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 (E. coli)

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Component #27: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #28: ligand, MAGNESIUM ION

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

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen Name: 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: 37 e/Å2 / Illumination Mode: OTHER
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 38000
3D reconstructionResolution: 4.8 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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