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Yorodumi- EMDB-37412: De novo transcribing complex 9 (AdML9G), the initially transcribi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37412 | |||||||||
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Title | De novo transcribing complex 9 (AdML9G), the initially transcribing complex with Pol II positioned 9nt downstream of TSS | |||||||||
Map data | ||||||||||
Sample |
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Keywords | transcribing complex / de novo transcription initiation / initially transcribing complex (ITC) / TRANSCRIPTION | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / synthetic construct (others) / Amanita phalloides (death cap) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.47 Å | |||||||||
Authors | Chen X / Liu W / Xu Y | |||||||||
Funding support | 1 items
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Citation | Journal: Science / Year: 2023 Title: Structural visualization of transcription initiation in action. Authors: Xizi Chen / Weida Liu / Qianmin Wang / Xinxin Wang / Yulei Ren / Xuechun Qu / Wanjun Li / Yanhui Xu / Abstract: Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted ...Transcription initiation is a complex process, and its mechanism is incompletely understood. We determined the structures of de novo transcribing complexes TC2 to TC17 with RNA polymerase II halted on G-less promoters when nascent RNAs reach 2 to 17 nucleotides in length, respectively. Connecting these structures generated a movie and a working model. As initially synthesized RNA grows, general transcription factors (GTFs) remain bound to the promoter and the transcription bubble expands. Nucleoside triphosphate (NTP)-driven RNA-DNA translocation and template-strand accumulation in a nearly sealed channel may promote the transition from initially transcribing complexes (ITCs) (TC2 to TC9) to early elongation complexes (EECs) (TC10 to TC17). Our study shows dynamic processes of transcription initiation and reveals why ITCs require GTFs and bubble expansion for initial RNA synthesis, whereas EECs need GTF dissociation from the promoter and bubble collapse for promoter escape. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37412.map.gz | 12.8 MB | EMDB map data format | |
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Header (meta data) | emd-37412-v30.xml emd-37412.xml | 32.7 KB 32.7 KB | Display Display | EMDB header |
Images | emd_37412.png | 66.9 KB | ||
Filedesc metadata | emd-37412.cif.gz | 4.6 KB | ||
Others | emd_37412_additional_1.map.gz emd_37412_half_map_1.map.gz emd_37412_half_map_2.map.gz | 2.8 MB 112.5 MB 112.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37412 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37412 | HTTPS FTP |
-Related structure data
Related structure data | 8wakC 8walC 8wanC 8waoC 8wapC 8waqC 8warC 8wasC 8watC 8wauC 8wavC 8wawC 8waxC 8wayC 8wazC 8wb0C C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37412.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.334 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Pol II module of AdML9G
File | emd_37412_additional_1.map | ||||||||||||
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Annotation | Pol II module of AdML9G | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37412_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37412_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : De novo transcribing complex 9 (AdML9G), the initially transcribi...
+Supramolecule #1: De novo transcribing complex 9 (AdML9G), the initially transcribi...
+Supramolecule #2: TFIID
+Supramolecule #3: RNA POLYMERASE II
+Supramolecule #4: TFIIA
+Supramolecule #5: TFIIB
+Supramolecule #6: TFIIF
+Supramolecule #7: DNA
+Supramolecule #8: TFIIH
+Supramolecule #9: RNA
+Supramolecule #10: Alpha-amanitin
+Supramolecule #11: TFIIE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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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: 50.0 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: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 11.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2668 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |