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- EMDB-37409: De novo transcribing complex 15 (TC15), the early elongation comp... -
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Open data
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Basic information
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Title | De novo transcribing complex 15 (TC15), the early elongation complex with Pol II positioned 15nt downstream of TSS | |||||||||
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![]() | transcribing complex / de novo transcription initiation / early elongation complex (EEC) / TRANSCRIPTION | |||||||||
Function / homology | ![]() phosphatase activator activity / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 ...phosphatase activator activity / TFIIF-class transcription factor complex binding / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 - Major Pathway / 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 / transcription factor TFIIF complex / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / FGFR2 alternative splicing / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / 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 / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / mRNA Capping / RNA polymerase III activity / 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 / mRNA Splicing - Minor Pathway / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / Tat-mediated elongation of the HIV-1 transcript / tRNA transcription by RNA polymerase III / RNA polymerase I activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / negative regulation of protein binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / P-body / response to virus / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cell junction / microtubule cytoskeleton / single-stranded DNA binding / protein phosphatase binding / toxin activity / Estrogen-dependent gene expression / nucleic acid binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / protein domain specific binding / intracellular membrane-bounded organelle Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
![]() | Chen X / Liu W / Wang Q / Wang X / Ren Y / Qu X / Li 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) | ![]() ![]() | 47.9 KB 47.9 KB | Display Display | ![]() |
Images | ![]() | 128.2 KB | ||
Filedesc metadata | ![]() | 10.9 KB | ||
Others | ![]() ![]() ![]() | 74.1 MB 70 MB 70 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8wayMC ![]() 8wakC ![]() 8walC ![]() 8wanC ![]() 8waoC ![]() 8wapC ![]() 8waqC ![]() 8warC ![]() 8wasC ![]() 8watC ![]() 8wauC ![]() 8wavC ![]() 8wawC ![]() 8waxC ![]() 8wazC ![]() 8wb0C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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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 TC15
File | emd_37409_additional_1.map | ||||||||||||
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Annotation | Overall map of TC15 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37409_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37409_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Structure of transcribing complex 15 (TC15), the early elongation...
+Supramolecule #1: Structure of transcribing complex 15 (TC15), the early elongation...
+Supramolecule #2: RNA POLYMERASE II
+Supramolecule #3: TFIIF
+Supramolecule #4: DNA
+Supramolecule #5: RNA
+Supramolecule #6: Alpha-amanitin
+Macromolecule #1: Alpha-amanitin
+Macromolecule #2: General transcription factor IIF subunit 1
+Macromolecule #3: General transcription factor IIF subunit 2
+Macromolecule #7: DNA-directed RNA polymerase subunit
+Macromolecule #8: DNA-directed RNA polymerase subunit beta
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #10: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #11: DNA-directed RNA polymerase II subunit E
+Macromolecule #12: DNA-directed RNA polymerase II subunit F
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #14: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #18: RPB12
+Macromolecule #4: non-template DNA
+Macromolecule #5: template DNA
+Macromolecule #6: RNA
+Macromolecule #19: ZINC ION
+Macromolecule #20: MAGNESIUM ION
+Macromolecule #21: [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-pur...
-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: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 119942 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |