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Basic information

Entry
Database: EMDB / ID: EMD-3378
TitleTranscription initiation complex structures elucidate DNA opening (OC3)
Map dataunsharpened OC3 map
Sample
  • Sample: yeast Pol II transcription initiation complex (open DNA)
  • Protein or peptide: DNA-directed RNA polymerase II
  • Protein or peptide: Transcription Factor IIA
  • Protein or peptide: Transcription Factor IIB
  • Protein or peptide: TATA-box-binding protein
  • Protein or peptide: Transcription Factor IIE
  • Protein or peptide: Transcription Factor IIF
  • DNA: synthetic promoter DNA construct (open)
KeywordsGene expression / Transcription initiation
Function / homology
Function and homology information


: / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / transcription factor TFIIE complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / TFIIF-class transcription factor complex binding ...: / transcription open complex formation at RNA polymerase II promoter / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RNA polymerase III preinitiation complex assembly / transcription factor TFIIIB complex / transcription factor TFIIE complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / TFIIF-class transcription factor complex binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / RPB4-RPB7 complex / DNA binding, bending / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / transcription factor TFIID complex / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA polymerase II general transcription initiation factor activity / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / Estrogen-dependent gene expression / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / termination of RNA polymerase II transcription / RNA polymerase II complex binding / Gap-filling DNA repair synthesis and ligation in TC-NER / protein phosphatase activator activity / termination of RNA polymerase I transcription / Dual incision in TC-NER / transcription by RNA polymerase III / positive regulation of transcription initiation by RNA polymerase II / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / positive regulation of translational initiation / nuclear-transcribed mRNA catabolic process / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / transcription elongation by RNA polymerase I / translesion synthesis / transcription-coupled nucleotide-excision repair / translation initiation factor binding / TBP-class protein binding / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / P-body / transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / ribonucleoside binding / mRNA processing / disordered domain specific binding / cytoplasmic stress granule / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / peroxisome / single-stranded DNA binding / ribosome biogenesis / DNA-binding transcription factor binding / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / protein dimerization activity / single-stranded RNA binding / negative regulation of DNA-templated transcription / nucleotide binding / mRNA binding / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / zinc ion binding
Similarity search - Function
: / Tfa2 E-tether / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain ...: / Tfa2 E-tether / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / TFIIE alpha subunit / TFE/IIEalpha-type HTH domain profile. / Transcription initiation factor IIE / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, beta-barrel / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / 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 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / Cyclin-like superfamily / 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 / Zinc finger TFIIS-type signature. / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / 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 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase, subunit RPB6 / : / 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. / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA directed RNA polymerase, 7 kDa subunit / Zinc finger, TFIIS-type
Similarity search - Domain/homology
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 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 ...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 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Transcription initiation factor IIA large subunit / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIE subunit alpha / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.35 Å
AuthorsPlaschka C / Hantsche M / Dienemann C / Burzinski C / Plitzko J / Cramer P
CitationJournal: Nature / Year: 2016
Title: Transcription initiation complex structures elucidate DNA opening.
Authors: C Plaschka / M Hantsche / C Dienemann / C Burzinski / J Plitzko / P Cramer /
Abstract: Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) ...Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.
History
DepositionMar 9, 2016-
Header (metadata) releaseApr 13, 2016-
Map releaseMay 18, 2016-
UpdateJun 15, 2016-
Current statusJun 15, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0325
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0325
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fyw
  • Surface level: 0.0325
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3378.png

Downloads & links

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Map

FileDownload / File: emd_3378.map.gz / Format: CCP4 / Size: 100.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened OC3 map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å		1.35 Å/pix.
x 300 pix.
= 405. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0325 / Movie #1: 0.0325
Minimum - Maximum-0.0392752 - 0.09277353
Average (Standard dev.)-0.00005954 (±0.00432831)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z405.000405.000405.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0390.093-0.000

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Supplemental data

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Sample components

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Entire : yeast Pol II transcription initiation complex (open DNA)

EntireName: yeast Pol II transcription initiation complex (open DNA)
Components
  • Sample: yeast Pol II transcription initiation complex (open DNA)
  • Protein or peptide: DNA-directed RNA polymerase II
  • Protein or peptide: Transcription Factor IIA
  • Protein or peptide: Transcription Factor IIB
  • Protein or peptide: TATA-box-binding protein
  • Protein or peptide: Transcription Factor IIE
  • Protein or peptide: Transcription Factor IIF
  • DNA: synthetic promoter DNA construct (open)

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Supramolecule #1000: yeast Pol II transcription initiation complex (open DNA)

SupramoleculeName: yeast Pol II transcription initiation complex (open DNA)
type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 7
Molecular weightTheoretical: 890 KDa

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Macromolecule #1: DNA-directed RNA polymerase II

MacromoleculeName: DNA-directed RNA polymerase II / type: protein_or_peptide / ID: 1 / Name.synonym: RNA polymerase II / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast
Molecular weightTheoretical: 513 KDa

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Macromolecule #2: Transcription Factor IIA

MacromoleculeName: Transcription Factor IIA / type: protein_or_peptide / ID: 2 / Name.synonym: TFIIA / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 45 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pOPINE

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Macromolecule #3: Transcription Factor IIB

MacromoleculeName: Transcription Factor IIB / type: protein_or_peptide / ID: 3 / Name.synonym: TFIIB / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 38 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pET21b

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Macromolecule #4: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 4 / Name.synonym: TBP, SPT15 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 27 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pOPINE

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Macromolecule #5: Transcription Factor IIE

MacromoleculeName: Transcription Factor IIE / type: protein_or_peptide / ID: 5 / Name.synonym: TFIIE / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 91 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pET21

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Macromolecule #6: Transcription Factor IIF

MacromoleculeName: Transcription Factor IIF / type: protein_or_peptide / ID: 6 / Name.synonym: TFIIF / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast
Molecular weightTheoretical: 129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)RIL / Recombinant plasmid: pETDuet-1

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Macromolecule #7: synthetic promoter DNA construct (open)

MacromoleculeName: synthetic promoter DNA construct (open) / type: dna / ID: 7 / Details: Contains a 15 nucleotide mismatch bubble / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: unidentified (others)
Molecular weightTheoretical: 44 KDa

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Details: 25 mM HEPES-KOH pH 7.5, 150 mM potassium acetate, 2 mM MgCl2, 5 mM DTT
GridDetails: R3.5/1 holey carbon grids (Quantifoil)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: Quantifoil R 3.5/1 holey carbon grids were glow-discharged before deposition of 4.5 microliters of sample. Grids were then blotted for 8.5 s and plunge-frozen in liquid ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateApr 26, 2016
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 1756 / Average electron dose: 33 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 4.2 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: 4.35 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 11231

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