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- EMDB-12721: Yeast TFIIH in the contracted state within the pre-initiation complex -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12721 | ||||||||||||||||||
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Title | Yeast TFIIH in the contracted state within the pre-initiation complex | ||||||||||||||||||
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Function / homology | ![]() regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter ...regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / transcription factor TFIIK complex / transcription open complex formation at RNA polymerase II promoter / RPB4-RPB7 complex / TFIIH-class transcription factor complex binding / phosphatidylinositol-3-phosphate binding / DNA 3'-5' helicase / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / DNA duplex unwinding / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / 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-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / transcription initiation at RNA polymerase III promoter / 3'-5' DNA helicase activity / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / ATPase activator activity / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / ATP-dependent activity, acting on DNA / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / translesion synthesis / RNA polymerase I activity / RNA polymerase II activity / DNA helicase activity / translation initiation factor binding / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / P-body / ribonucleoside binding / cytoplasmic stress granule / DNA-directed RNA polymerase / ubiquitin protein ligase activity / ribosome biogenesis / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / single-stranded RNA binding / DNA repair / nucleotide binding / mRNA binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||||||||
![]() | Schilbach S / Aibara S / Dienemann C / Grabbe F / Cramer P | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. Authors: Sandra Schilbach / Shintaro Aibara / Christian Dienemann / Frauke Grabbe / Patrick Cramer / ![]() Abstract: Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of ...Transcription initiation requires assembly of the RNA polymerase II (Pol II) pre-initiation complex (PIC) and opening of promoter DNA. Here, we present the long-sought high-resolution structure of the yeast PIC and define the mechanism of initial DNA opening. We trap the PIC in an intermediate state that contains half a turn of open DNA located 30-35 base pairs downstream of the TATA box. The initially opened DNA region is flanked and stabilized by the polymerase "clamp head loop" and the TFIIF "charged region" that both contribute to promoter-initiated transcription. TFIIE facilitates initiation by buttressing the clamp head loop and by regulating the TFIIH translocase. The initial DNA bubble is then extended in the upstream direction, leading to the open promoter complex and enabling start-site scanning and RNA synthesis. This unique mechanism of DNA opening may permit more intricate regulation than in the Pol I and Pol III systems. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
-Validation report
Summary document | ![]() | 359.9 KB | Display | ![]() |
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Full document | ![]() | 359 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7o4kMC ![]() 7o4iC ![]() 7o4jC ![]() 7o4lC ![]() 7o72C ![]() 7o73C ![]() 7o75C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Additional map: Locally filtered map (non-composite) of a refinement of...
+Additional map: Half-map 2 of focused refinement encompassing the Tfb2...
+Additional map: Half-map 2 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+Additional map: Half-map 1 of focused refinement encompassing the Tfb2...
+Additional map: Half-map 1 of focused refinement encompassing the Ssl2/Tfb2/Tfb5...
+Additional map: Half-map 1 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Tfb3-RING-finger/TFIIE/Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 2 of focused refinement encompassing the Pol...
+Additional map: Half-map 1 of focused refinement encompassing the Rad3/Ssl1...
+Additional map: Half-map 2 of focused refinement encompassing the Rad3/Ssl1...
+Additional map: Half-map 1 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle...
+Additional map: Half-map 2 of focused refinement encompassing the Ssl1/Tfb4-eZnF/Tfb1-3-helix-bundle...
+Half map: #2
+Half map: #1
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Sample components
+Entire : Yeast TFIIH in the contracted state within the pre-initiation complex
+Supramolecule #1: Yeast TFIIH in the contracted state within the pre-initiation complex
+Macromolecule #1: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #2: General transcription and DNA repair factor IIH subunit TFB1
+Macromolecule #3: General transcription and DNA repair factor IIH subunit TFB2
+Macromolecule #4: RNA polymerase II transcription factor B subunit 3
+Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #6: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #7: General transcription and DNA repair factor IIH subunit SSL1
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #10: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #16: Transcription initiation factor IIE subunit alpha
+Macromolecule #17: Transcription initiation factor IIE subunit beta
+Macromolecule #14: Non-template DNA
+Macromolecule #15: Template DNA
+Macromolecule #18: IRON/SULFUR CLUSTER
+Macromolecule #19: ZINC ION
+Macromolecule #20: BERYLLIUM TRIFLUORIDE ION
+Macromolecule #21: MAGNESIUM ION
+Macromolecule #22: ADENOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 29670 / Average exposure time: 9.0 sec. / Average electron dose: 43.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |