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Yorodumi- EMDB-19719: RNA polymerase II core initially transcribing complex with an ord... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19719 | |||||||||
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Title | RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA polymerase II / promoter escape / de novo transcription / TRANSCRIPTION | |||||||||
Function / homology | Function and homology information positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / RNA polymerase transcription factor SL1 complex / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RNA polymerase I core promoter sequence-specific DNA binding ...positive regulation of core promoter binding / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / RNA polymerase transcription factor SL1 complex / transcription factor TFIIE complex / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Signaling by FGFR2 IIIa TM / Viral Messenger RNA Synthesis / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / protein acetylation / cell division site / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / RNA polymerase II complex binding / mRNA Splicing - Minor Pathway / acetyltransferase activity / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / viral transcription / aryl hydrocarbon receptor binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / transcription by RNA polymerase III / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II core promoter sequence-specific DNA binding / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / spindle assembly / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / core promoter sequence-specific DNA binding Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / unidentified adenovirus / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Zhan Y / Grabbe F / Oberbeckmann E / Dienemann C / Cramer P | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Three-step mechanism of promoter escape by RNA polymerase II. Authors: Yumeng Zhan / Frauke Grabbe / Elisa Oberbeckmann / Christian Dienemann / Patrick Cramer / Abstract: The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how ...The transition from transcription initiation to elongation is highly regulated in human cells but remains incompletely understood at the structural level. In particular, it is unclear how interactions between RNA polymerase II (RNA Pol II) and initiation factors are broken to enable promoter escape. Here, we reconstitute RNA Pol II promoter escape in vitro and determine high-resolution structures of initially transcribing complexes containing 8-, 10-, and 12-nt ordered RNAs and two elongation complexes containing 14-nt RNAs. We suggest that promoter escape occurs in three major steps. First, the growing RNA displaces the B-reader element of the initiation factor TFIIB without evicting TFIIB. Second, the rewinding of the transcription bubble coincides with the eviction of TFIIA, TFIIB, and TBP. Third, the binding of DSIF and NELF facilitates TFIIE and TFIIH dissociation, establishing the paused elongation complex. This three-step model for promoter escape fills a gap in our understanding of the initiation-elongation transition of RNA Pol II transcription. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19719.map.gz | 214.6 MB | EMDB map data format | |
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Header (meta data) | emd-19719-v30.xml emd-19719.xml | 46.5 KB 46.5 KB | Display Display | EMDB header |
Images | emd_19719.png | 121.1 KB | ||
Masks | emd_19719_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-19719.cif.gz | 11.9 KB | ||
Others | emd_19719_half_map_1.map.gz emd_19719_half_map_2.map.gz | 193.9 MB 193.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19719 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19719 | HTTPS FTP |
-Validation report
Summary document | emd_19719_validation.pdf.gz | 812 KB | Display | EMDB validaton report |
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Full document | emd_19719_full_validation.pdf.gz | 811.5 KB | Display | |
Data in XML | emd_19719_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | emd_19719_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19719 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19719 | HTTPS FTP |
-Related structure data
Related structure data | 8s52MC 8s51C 8s54C 8s55C 8s5nC 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_19719.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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:
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-Supplemental data
-Mask #1
File | emd_19719_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19719_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19719_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Core initially transcribing complex with an ordered RNA of 10 nt
+Supramolecule #1: Core initially transcribing complex with an ordered RNA of 10 nt
+Supramolecule #2: RNA polymerase II
+Supramolecule #3: DNA and RNA
+Supramolecule #4: TATA-box-binding protein, Transcription initiation factor IIB, II...
+Supramolecule #5: Transcription initiation factor IIA
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: RNA polymerase II subunit D
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: Transcription initiation factor IIB
+Macromolecule #15: TATA-box-binding protein
+Macromolecule #17: General transcription factor IIF subunit 1
+Macromolecule #18: General transcription factor IIF subunit 2
+Macromolecule #20: Transcription initiation factor IIA subunit 1
+Macromolecule #21: Transcription initiation factor IIA subunit 2
+Macromolecule #22: General transcription factor IIE subunit 1
+Macromolecule #23: Transcription initiation factor IIE subunit beta
+Macromolecule #14: Non-template DNA
+Macromolecule #19: Template DNA
+Macromolecule #16: RNA
+Macromolecule #24: ZINC ION
+Macromolecule #25: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 151975 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |