+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23907 | ||||||||||||||||||
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Title | General transcription factor TFIIH (weak binding) | ||||||||||||||||||
Map data | TFIIH (weak binding) | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information regulation of mitotic recombination / RNA polymerase II promoter clearance / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / DNA 3'-5' helicase / transcription factor TFIIH core complex ...regulation of mitotic recombination / RNA polymerase II promoter clearance / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / DNA translocase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / DNA 3'-5' helicase / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / transcription factor TFIIH holo complex / transcription preinitiation complex / DNA duplex unwinding / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 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 / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / 3'-5' DNA helicase activity / Gap-filling DNA repair synthesis and ligation in TC-NER / ATPase activator activity / Dual incision in TC-NER / DNA helicase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / double-stranded DNA binding / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.6 Å | ||||||||||||||||||
Authors | Yang C / Fujiwara R / Kim HJ / Gorbea Colon JJ / Steimle S / Garcia BA / Murakami K | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural visualization of de novo transcription initiation by Saccharomyces cerevisiae RNA polymerase II. Authors: Chun Yang / Rina Fujiwara / Hee Jong Kim / Pratik Basnet / Yunye Zhu / Jose J Gorbea Colón / Stefan Steimle / Benjamin A Garcia / Craig D Kaplan / Kenji Murakami / Abstract: Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous ...Previous structural studies of the initiation-elongation transition of RNA polymerase II (pol II) transcription have relied on the use of synthetic oligonucleotides, often artificially discontinuous to capture pol II in the initiating state. Here, we report multiple structures of initiation complexes converted de novo from a 33-subunit yeast pre-initiation complex (PIC) through catalytic activities and subsequently stalled at different template positions. We determine that PICs in the initially transcribing complex (ITC) can synthesize a transcript of ∼26 nucleotides before transitioning to an elongation complex (EC) as determined by the loss of general transcription factors (GTFs). Unexpectedly, transition to an EC was greatly accelerated when an ITC encountered a downstream EC stalled at promoter proximal regions and resulted in a collided head-to-end dimeric EC complex. Our structural analysis reveals a dynamic state of TFIIH, the largest of GTFs, in PIC/ITC with distinct functional consequences at multiple steps on the pathway to elongation. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23907.map.gz | 24.2 MB | EMDB map data format | |
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Header (meta data) | emd-23907-v30.xml emd-23907.xml | 24.1 KB 24.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23907_fsc.xml | 9 KB | Display | FSC data file |
Images | emd_23907.png | 38.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23907 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23907 | HTTPS FTP |
-Validation report
Summary document | emd_23907_validation.pdf.gz | 372.8 KB | Display | EMDB validaton report |
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Full document | emd_23907_full_validation.pdf.gz | 372.4 KB | Display | |
Data in XML | emd_23907_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | emd_23907_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23907 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23907 | HTTPS FTP |
-Related structure data
Related structure data | 7ml3MC 7meiC 7mk9C 7mkaC 7ml0C 7ml1C 7ml2C 7ml4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10865 (Title: Structural visualization of de novo initiation of RNA polymerase II transcription Data size: 14.3 TB Data #1: raw micrographs for PIC + ITC maps [micrographs - multiframe] Data #2: raw micrographs for EC+EC map [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23907.map.gz / Format: CCP4 / Size: 65.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | TFIIH (weak binding) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : General transcription factor TFIIH (weak binding)
+Supramolecule #1: General transcription factor TFIIH (weak binding)
+Macromolecule #1: BJ4_G0050160.mRNA.1.CDS.1
+Macromolecule #2: RNA polymerase II transcription factor B subunit 2
+Macromolecule #3: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #4: Tfb1
+Macromolecule #5: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #6: General transcription and DNA repair factor IIH
+Macromolecule #7: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #9: non-template strand DNA
+Macromolecule #10: template strand DNA
+Macromolecule #11: ZINC ION
+Macromolecule #12: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |