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Open data
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Basic information
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Title | Human RNA Polymerase III de novo transcribing complex 4 (TC4) | |||||||||
![]() | Pol III TC4 main map | |||||||||
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![]() | initiation transcribing complex / TRANSCRIPTION/DNA/RNA / TRANSCRIPTION-DNA-RNA complex | |||||||||
Function / homology | ![]() snRNA-activating protein complex / snRNA transcription / transcription preinitiation complex assembly / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III preinitiation complex assembly / RNA Polymerase III Chain Elongation / TFIIIC-class transcription factor complex binding / transcription factor TFIIIB complex / RNA Polymerase III Transcription Termination ...snRNA-activating protein complex / snRNA transcription / transcription preinitiation complex assembly / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III preinitiation complex assembly / RNA Polymerase III Chain Elongation / TFIIIC-class transcription factor complex binding / transcription factor TFIIIB complex / RNA Polymerase III Transcription Termination / calcitonin gene-related peptide receptor activity / DNA/RNA hybrid binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / regulation of transcription by RNA polymerase I / regulation of transcription by RNA polymerase III / RNA polymerase III general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RPAP3/R2TP/prefoldin-like complex / DNA polymerase III complex / 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 / Cytosolic sensors of pathogen-associated DNA / transcription factor TFIIA complex / female germ cell nucleus / RNA Polymerase III Abortive And Retractive Initiation / male pronucleus / positive regulation of innate immune response / female pronucleus / RNA polymerase II general transcription initiation factor binding / nucleobase-containing compound metabolic process / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / RNA Polymerase I Transcription Termination / transcription preinitiation complex / MicroRNA (miRNA) biogenesis / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / 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 / transcription initiation at RNA polymerase III promoter / mRNA Splicing - Minor Pathway / PIWI-interacting RNA (piRNA) biogenesis / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / RNA Polymerase I Transcription Initiation / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of transcription initiation by RNA polymerase II / neuropeptide signaling pathway / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase III complex / core promoter sequence-specific DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Transcription Elongation / : / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / DNA-directed RNA polymerase activity / Inhibition of DNA recombination at telomere / mRNA Splicing - Major Pathway / positive regulation of interferon-beta production / male germ cell nucleus / acrosomal vesicle / SIRT1 negatively regulates rRNA expression / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / DNA-templated transcription initiation / Transcriptional regulation by small RNAs / mRNA transcription by RNA polymerase II / euchromatin Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
![]() | Wang Q / Ren Y / Jin Q / Chen X / Xu Y | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structural insights into human Pol III transcription initiation in action. Authors: Qianmin Wang / Yulei Ren / Qianwei Jin / Xizi Chen / Yanhui Xu / ![]() Abstract: RNA polymerase III (Pol III) transcribes highly demanded RNAs grouped into three types of classical promoters, including type 1 (5S rRNA), type 2 (tRNA) and type 3 (short non-coding RNAs, such as U6, ...RNA polymerase III (Pol III) transcribes highly demanded RNAs grouped into three types of classical promoters, including type 1 (5S rRNA), type 2 (tRNA) and type 3 (short non-coding RNAs, such as U6, 7SK and RNase H1) promoters. While structures of the Pol III preinitiation complex (PIC) and elongation complex (EC) have been determined, the mechanism underlying the transition from initiation to elongation remains unclear. Here we reconstituted seven human Pol III transcribing complexes (TC4, TC5, TC6, TC8, TC10, TC12 and TC13) halted on U6 promoters with nascent RNAs of 4-13 nucleotides. Cryo-electron microscopy structures captured initially transcribing complexes (ITCs; TC4 and TC5) and ECs (TC6-13). Together with KMnO footprinting, the data reveal extensive modular rearrangements: the transcription bubble expands from PIC to TC5, followed by general transcription factor (GTF) dissociation and abrupt bubble collapse from TC5 to TC6, marking the ITC-EC transition. In TC5, SNAPc and TFIIIB remain bound to the promoter and Pol III, while the RNA-DNA hybrid adopts a tilted conformation with template DNA blocked by BRF2, a TFIIIB subunit. Hybrid forward translocation during ITC-EC transition triggers BRF2-finger retraction, GTF release and transcription-bubble collapse. Pol III then escapes the promoter while GTFs stay bound upstream, potentially enabling reinitiation. These findings reveal molecular insights into Pol III dynamics and reinitiation mechanisms on type 3 promoters of highly demanded small RNAs, with the earliest documented initiation-elongation transition for an RNA polymerase. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 60.3 KB 60.3 KB | Display Display | ![]() |
Images | ![]() | 110.5 KB | ||
Filedesc metadata | ![]() | 15.5 KB | ||
Others | ![]() ![]() ![]() ![]() | 118.1 MB 115.2 MB 118.4 MB 118.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9k3vMC ![]() 9k2gC ![]() 9k36C ![]() 9k38C ![]() 9k39C ![]() 9k3bC ![]() 9k3uC ![]() 9lktC ![]() 9lxnC ![]() 9lxoC M: atomic model generated by this map C: citing same article ( |
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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
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Annotation | Pol III TC4 main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.33254 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: SNAPC-TFIIIB-U6 local map
File | emd_62030_additional_1.map | ||||||||||||
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Annotation | SNAPC-TFIIIB-U6 local map | ||||||||||||
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Density Histograms |
-Additional map: Pol III TC4 postprocess map
File | emd_62030_additional_2.map | ||||||||||||
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Annotation | Pol III TC4 postprocess map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Pol III TC4 half map1
File | emd_62030_half_map_1.map | ||||||||||||
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Annotation | Pol III TC4 half map1 | ||||||||||||
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Density Histograms |
-Half map: Pol III TC4 half map2
File | emd_62030_half_map_2.map | ||||||||||||
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Annotation | Pol III TC4 half map2 | ||||||||||||
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Density Histograms |
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Sample components
+Entire : RNA polymerase III transcribing complex 4
+Supramolecule #1: RNA polymerase III transcribing complex 4
+Macromolecule #1: snRNA-activating protein complex subunit 1
+Macromolecule #2: snRNA-activating protein complex subunit 3
+Macromolecule #3: snRNA-activating protein complex subunit 4
+Macromolecule #4: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #5: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #6: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #7: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #10: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #12: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #13: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #14: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #15: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #18: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #19: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #20: DNA-directed RNA polymerase III subunit RPC7
+Macromolecule #21: TATA-box-binding protein
+Macromolecule #22: Transcription factor IIIB 50 kDa subunit
+Macromolecule #23: Transcription factor TFIIIB component B'' homolog
+Macromolecule #24: DNA (96-MER)
+Macromolecule #25: DNA (96-MER)
+Macromolecule #26: RNA (5'-R(P*UP*GP*C)-3')
+Macromolecule #27: ZINC ION
+Macromolecule #28: 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #29: IRON/SULFUR CLUSTER
+Macromolecule #30: MAGNESIUM ION
+Macromolecule #31: GUANOSINE-5'-TRIPHOSPHATE
-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: 8 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | TFS 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: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |