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Open data
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Basic information
Entry | Database: PDB / ID: 6cnc | |||||||||||||||||||||
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Title | Yeast RNA polymerase III open complex | |||||||||||||||||||||
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![]() | transcription/dna / ![]() ![]() ![]() | |||||||||||||||||||||
Function / homology | ![]() RNA polymerase III core binding / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity ...RNA polymerase III core binding / TFIIA-class transcription factor complex binding / RNA polymerase III transcription regulatory region sequence-specific DNA binding / DNA-templated transcription open complex formation / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / TFIIIC-class transcription factor complex binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase III general transcription initiation factor activity / regulation of transcription by RNA polymerase III / transcription factor TFIIA complex / RNA polymerase I preinitiation complex assembly / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 838.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7531MC ![]() 7530C ![]() 7532C ![]() 7533C ![]() 7534C ![]() 6cnbC ![]() 6cndC ![]() 6cnfC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-DNA-directed RNA polymerase III subunit ... , 10 types, 10 molecules ABDGIMNOPQ
#1: Protein | ![]() Mass: 162517.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P04051, ![]() |
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#2: Protein | ![]() Mass: 129629.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P22276, ![]() |
#4: Protein | ![]() Mass: 18623.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P47076 |
#7: Protein | ![]() Mass: 24349.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P35718 |
#9: Protein | ![]() Mass: 12525.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: Q04307 |
#13: Protein | ![]() Mass: 32178.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P36121 |
#14: Protein | ![]() Mass: 46751.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P25441 |
#15: Protein | ![]() Mass: 74112.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32349 |
#16: Protein | ![]() Mass: 36174.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P32910 |
#17: Protein | ![]() Mass: 27299.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P17890 |
-DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK
#3: Protein | Mass: 37732.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P07703 |
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#11: Protein | Mass: 16167.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P28000 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#5: Protein | ![]() Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P20434 |
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#6: Protein | ![]() Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P20435 |
#8: Protein | ![]() Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P20436 |
#10: Protein | ![]() Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P22139 |
#12: Protein | ![]() Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / References: UniProt: P40422 |
-Transcription factor ... , 2 types, 2 molecules RS
#18: Protein | Mass: 82097.867 Da / Num. of mol.: 1 / Mutation: C438S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BRF1, PCF4, TDS4, YGR246C, SPT15, BTF1, TBP1, YER148W / Production host: ![]() ![]() ![]() |
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#19: Protein | Mass: 66249.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: BDP1, TFC5, YNL039W, N2682 / Production host: ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules XY
#20: DNA chain | Mass: 21807.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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#21: DNA chain | Mass: 21894.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-Non-polymers , 1 types, 7 molecules ![](data/chem/img/ZN.gif)
#22: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: Yeast RNA polymerase III open complex / Type: COMPLEX / Entity ID: #1-#21 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.9 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FS |
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Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Image recording | Electron dose: 68.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Details: CTF amplitude correction was performed following 3D auto refinement in relion. Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74281 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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