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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7532 | |||||||||||||||||||||
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Title | Yeast RNA polymerase III natural open complex (nOC) | |||||||||||||||||||||
![]() | Yeast RNA polymerase III natural open complex (nOC) | |||||||||||||||||||||
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Function / homology | ![]() RNA polymerase III core binding / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding ...RNA polymerase III core binding / TFIIA-class transcription factor complex binding / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / transcription preinitiation complex / DNA binding, bending / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / 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 factor TFIID complex / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / TBP-class protein binding / nucleotidyltransferase activity / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / disordered domain specific binding / ribosome biogenesis / peroxisome / single-stranded DNA binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleotide binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | |||||||||||||||||||||
![]() | Han Y / He Y | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural visualization of RNA polymerase III transcription machineries. Authors: Yan Han / Chunli Yan / Susan Fishbain / Ivaylo Ivanov / Yuan He / ![]() Abstract: RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre- ...RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III-TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft. The architecture of Pol III PIC more resembles that of the Pol II PIC than the Pol I PIC. In addition, we also obtain a 3D reconstruction of Pol III in complex with TFIIIB using the elongation complex (EC) scaffold, shedding light on the mechanism of facilitated recycling of Pol III prior to transcription re-initiation. | |||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 54.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 37.3 KB 37.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.3 KB | Display | ![]() |
Images | ![]() | 201.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cndMC ![]() 7530C ![]() 7531C ![]() 7533C ![]() 7534C ![]() 6cnbC ![]() 6cncC ![]() 6cnfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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 | Yeast RNA polymerase III natural open complex (nOC) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Yeast RNA polymerase III natural open complex (nOC)
+Supramolecule #1: Yeast RNA polymerase III natural open complex (nOC)
+Macromolecule #1: DNA-directed RNA polymerase III subunit RPC1
+Macromolecule #2: DNA-directed RNA polymerase III subunit RPC2
+Macromolecule #3: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #4: DNA-directed RNA polymerase III subunit RPC9
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #7: DNA-directed RNA polymerase III subunit RPC8
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase III subunit RPC10
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #13: DNA-directed RNA polymerase III subunit RPC5
+Macromolecule #14: DNA-directed RNA polymerase III subunit RPC4
+Macromolecule #15: DNA-directed RNA polymerase III subunit RPC3
+Macromolecule #16: DNA-directed RNA polymerase III subunit RPC6
+Macromolecule #17: DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA pol...
+Macromolecule #18: Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein...
+Macromolecule #19: Transcription factor TFIIIB component B'',Transcription factor TF...
+Macromolecule #20: DNA (71-MER)
+Macromolecule #21: DNA (71-MER)
+Macromolecule #22: ZINC ION
-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 / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL 3200FS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 68.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |