+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23905 | ||||||||||||||||||
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Title | RNA polymerase II pre-initiation complex (PIC2) | ||||||||||||||||||
Map data | PIC2 | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information : / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / : / TFIIH-class transcription factor complex binding ...: / regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / : / TFIIH-class transcription factor complex binding / positive regulation of mitotic recombination / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / DNA 3'-5' helicase / transcription preinitiation complex / DNA binding, bending / DNA duplex unwinding / 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 / 3'-5' DNA helicase activity / 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 / transcription factor TFIID complex / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / Formation of TC-NER Pre-Incision Complex / RNA polymerase III activity / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / ATPase activator activity / RNA polymerase II activity / Dual incision in TC-NER / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / TBP-class protein binding / DNA helicase activity / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / disordered domain specific binding / double-stranded DNA binding / single-stranded DNA binding / DNA-binding transcription factor binding / transcription regulator complex / DNA helicase / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / damaged DNA binding / single-stranded RNA binding / protein dimerization activity / negative regulation of DNA-templated transcription / chromatin binding / DNA-templated transcription / nucleotide binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription Similarity search - Function | ||||||||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 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_23905.map.gz | 37.9 MB | EMDB map data format | |
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Header (meta data) | emd-23905-v30.xml emd-23905.xml | 53.3 KB 53.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23905_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_23905.png | 47.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23905 | HTTPS FTP |
-Validation report
Summary document | emd_23905_validation.pdf.gz | 348.2 KB | Display | EMDB validaton report |
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Full document | emd_23905_full_validation.pdf.gz | 347.7 KB | Display | |
Data in XML | emd_23905_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | emd_23905_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23905 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23905 | HTTPS FTP |
-Related structure data
Related structure data | 7ml1MC 7meiC 7mk9C 7mkaC 7ml0C 7ml2C 7ml3C 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_23905.map.gz / Format: CCP4 / Size: 247.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PIC2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : RNA polymerase II pre-initiation complex (PIC2)
+Supramolecule #1: RNA polymerase II pre-initiation complex (PIC2)
+Supramolecule #2: Pol II + TFIIB
+Supramolecule #3: DNA+TFIIA+TFIIE+TFIIF
+Supramolecule #4: TFIIH
+Macromolecule #1: Tfb1
+Macromolecule #2: General transcription and DNA repair factor IIH subunit TFB4
+Macromolecule #3: General transcription and DNA repair factor IIH helicase subunit XPD
+Macromolecule #4: General transcription and DNA repair factor IIH subunit SSL1
+Macromolecule #5: RNA polymerase II transcription factor B subunit 2
+Macromolecule #6: General transcription and DNA repair factor IIH subunit TFB5
+Macromolecule #7: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #8: BJ4_G0050160.mRNA.1.CDS.1
+Macromolecule #9: TATA-box-binding protein
+Macromolecule #12: DNA-directed RNA polymerase subunit
+Macromolecule #13: DNA-directed RNA polymerase subunit beta
+Macromolecule #14: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #17: DNA-directed RNA polymerases I,II,and III subunit RPABC2
+Macromolecule #18: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #19: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #20: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #21: DNA-directed RNA polymerases II subunit RPABC5
+Macromolecule #22: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #23: DNA-directed RNA polymerases II subunit RPABC4
+Macromolecule #24: Transcription initiation factor IIB
+Macromolecule #25: Transcription initiation factor IIF subunit alpha
+Macromolecule #26: Transcription initiation factor IIF subunit beta
+Macromolecule #27: Transcription initiation factor IIA large subunit
+Macromolecule #28: Transcription initiation factor IIA subunit 2
+Macromolecule #29: Transcription initiation factor IIE subunit alpha
+Macromolecule #30: Transcription initiation factor IIE subunit beta
+Macromolecule #10: non-template strand DNA
+Macromolecule #11: template strand DNA
+Macromolecule #31: ZINC ION
+Macromolecule #32: IRON/SULFUR CLUSTER
+Macromolecule #33: MAGNESIUM ION
-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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Grid | Model: Quantifoil R0.6/1 / Material: COPPER / Mesh: 200 |
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 |