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Yorodumi- EMDB-23887: Complex structure of trailing EC of EC+EC (trailing EC-focused) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23887 | |||||||||
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Title | Complex structure of trailing EC of EC+EC (trailing EC-focused) | |||||||||
Map data | The map of trailing EC with sharpening by post_processed in Relion | |||||||||
Sample |
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Function / homology | Function and homology information TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / : ...TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / Processing of Capped Intron-Containing Pre-mRNA / : / 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 Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / protein phosphatase activator activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase II, core complex / RNA polymerase I activity / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / nucleic acid binding / single-stranded RNA binding / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Baker's yeast (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Yang C / Murakami K | |||||||||
Funding support | 1 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_23887.map.gz | 9.4 MB | EMDB map data format | |
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Header (meta data) | emd-23887-v30.xml emd-23887.xml | 36.5 KB 36.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23887_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_23887.png | 74.5 KB | ||
Masks | emd_23887_msk_1.map | 40.6 MB | Mask map | |
Others | emd_23887_additional_1.map.gz emd_23887_half_map_1.map.gz emd_23887_half_map_2.map.gz | 31.2 MB 31.3 MB 31.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23887 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23887 | HTTPS FTP |
-Validation report
Summary document | emd_23887_validation.pdf.gz | 925.4 KB | Display | EMDB validaton report |
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Full document | emd_23887_full_validation.pdf.gz | 924.9 KB | Display | |
Data in XML | emd_23887_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_23887_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23887 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23887 | HTTPS FTP |
-Related structure data
Related structure data | 7mk9MC 7meiC 7mkaC 7ml0C 7ml1C 7ml2C 7ml3C 7ml4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23887.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | The map of trailing EC with sharpening by post_processed in Relion | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_23887_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: The map of trailing EC without sharpening
File | emd_23887_additional_1.map | ||||||||||||
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Annotation | The map of trailing EC without sharpening | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Trailing EC of EC+EC (trailing EC-focused) half map 1
File | emd_23887_half_map_1.map | ||||||||||||
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Annotation | Trailing EC of EC+EC (trailing EC-focused) half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Trailing EC of EC+EC (trailing EC-focused) half map 2
File | emd_23887_half_map_2.map | ||||||||||||
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Annotation | Trailing EC of EC+EC (trailing EC-focused) half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex structure of trailing EC of the EC+EC (trailing EC -focused)
+Supramolecule #1: Complex structure of trailing EC of the EC+EC (trailing EC -focused)
+Macromolecule #1: DNA (40-MER)
+Macromolecule #2: DNA (40-MER)
+Macromolecule #3: DNA-directed RNA polymerase subunit
+Macromolecule #4: DNA-directed RNA polymerase subunit beta
+Macromolecule #5: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #6: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #8: DNA-directed RNA polymerases I,II,and III subunit RPABC2
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #12: DNA-directed RNA polymerases II subunit RPABC5
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #14: DNA-directed RNA polymerases II subunit RPABC4
+Macromolecule #16: Transcription initiation factor IIF subunit alpha
+Macromolecule #17: Transcription initiation factor IIF subunit beta
+Macromolecule #15: RNA (5'-R(P*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*CP*CP*CP*AP*A)-3')
+Macromolecule #18: ZINC ION
+Macromolecule #19: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.6 / Details: 20 mM HEPES PH 7.6 50 mM KoAc 5 mM DTT 2 mM MgoAc |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |