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- EMDB-37413: De novo transcribing complex 10 (AdML10G), the early elongation c... -
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Open data
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Basic information
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Title | De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS. | |||||||||
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![]() | transcribing complex / de novo transcription initiation / early elongation complex (EEC) / TRANSCRIPTION | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.47 Å | |||||||||
![]() | Chen X / Liu W / Xu Y | |||||||||
Funding support | 1 items
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![]() | ![]() 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 | ![]() | 2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.3 KB 27.3 KB | Display Display | ![]() |
Images | ![]() | 127.3 KB | ||
Filedesc metadata | ![]() | 4.5 KB | ||
Others | ![]() ![]() ![]() | 74.2 MB 69.9 MB 69.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 808.3 KB | Display | ![]() |
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Full document | ![]() | 807.9 KB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 16.6 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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: Overall map of AdML10G
File | emd_37413_additional_1.map | ||||||||||||
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Annotation | Overall map of AdML10G | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37413_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37413_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : De novo transcribing complex 10 (AdML10G), the early elongation c...
Entire | Name: De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS. |
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Components |
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-Supramolecule #1: De novo transcribing complex 10 (AdML10G), the early elongation c...
Supramolecule | Name: De novo transcribing complex 10 (AdML10G), the early elongation complex with Pol II positioned 10nt downstream of TSS. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18 |
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-Supramolecule #2: RNA POLYMERASE II
Supramolecule | Name: RNA POLYMERASE II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #7-#18 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: TFIIF
Supramolecule | Name: TFIIF / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
-Supramolecule #4: DNA
Supramolecule | Name: DNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4-#5 |
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Source (natural) | Organism: synthetic construct (others) / Synthetically produced: Yes |
-Supramolecule #5: RNA
Supramolecule | Name: RNA / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #6 |
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Source (natural) | Organism: synthetic construct (others) / Synthetically produced: Yes |
-Supramolecule #6: Alpha-amanitin
Supramolecule | Name: Alpha-amanitin / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85241 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |