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Yorodumi- PDB-6rui: RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 -
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-Basic information
Entry | Database: PDB / ID: 6rui | ||||||
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Title | RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA Polymerase I / Pre-initiation complex / PIC / Open Complex / OC / Core Factor / CF / Rrn3 / DNA opening | ||||||
Function / homology | Function and homology information RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I preinitiation complex assembly / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA ...RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core binding / rDNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I preinitiation complex assembly / 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 / regulation of cell size / 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 / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / 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 I activity / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / TBP-class protein binding / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / ribonucleoside binding / DNA-directed RNA polymerase / ribosome biogenesis / peroxisome / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | synthetic construct (others) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||
Authors | Mueller, C.W. / Sadian, Y. / Tafur, L. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Molecular insight into RNA polymerase I promoter recognition and promoter melting. Authors: Yashar Sadian / Florence Baudin / Lucas Tafur / Brice Murciano / Rene Wetzel / Felix Weis / Christoph W Müller / Abstract: RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I ...RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 Å resolution to visualize Pol I promoter melting and to structurally and biochemically characterize the recognition mechanism of Pol I promoter DNA. In the closed complex, double-stranded DNA runs outside the DNA-binding cleft. Rotation of CF and upstream DNA with respect to Pol I and Rrn3 results in the spontaneous loading and opening of the promoter followed by cleft closure and positioning of the Pol I A49 tandem winged helix domain (tWH) onto DNA. Conformational rearrangement of A49 tWH leads to a clash with Rrn3 to initiate complex disassembly and promoter escape. Comprehensive insight into the Pol I transcription initiation cycle allows comparisons with promoter opening by Pol II and Pol III. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6rui.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6rui.ent.gz | 929.8 KB | Display | PDB format |
PDBx/mmJSON format | 6rui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rui_validation.pdf.gz | 946.1 KB | Display | wwPDB validaton report |
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Full document | 6rui_full_validation.pdf.gz | 1001.7 KB | Display | |
Data in XML | 6rui_validation.xml.gz | 151.2 KB | Display | |
Data in CIF | 6rui_validation.cif.gz | 236.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/6rui ftp://data.pdbj.org/pub/pdb/validation_reports/ru/6rui | HTTPS FTP |
-Related structure data
Related structure data | 10006MC 4982C 4984C 4985C 4987C 6rqhC 6rqlC 6rqtC 6rrdC 6ruoC 6rweC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA chain , 2 types, 2 molecules TU
#1: DNA chain | Mass: 21216.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
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#2: DNA chain | Mass: 21942.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-DNA-directed RNA polymerase I subunit ... , 7 types, 7 molecules INMABDG
#3: Protein | Mass: 13676.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA12, RRN4, YJR063W, J1747 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32529 |
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#4: Protein | Mass: 26933.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA34, YJL148W, J0637 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47006 |
#5: Protein | Mass: 46721.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA49, RRN13, YNL248C, N0880 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01080 |
#6: Protein | Mass: 186676.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA190, RPA1, RRN1, YOR341W, O6276 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10964, DNA-directed RNA polymerase |
#7: Protein | Mass: 135910.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA135, RPA2, RRN2, SRP3, YPR010C, YP9531.03C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22138, DNA-directed RNA polymerase |
#9: Protein | Mass: 14599.128 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA14, YDR156W, YD8358.11 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P50106 |
#12: Protein | Mass: 36264.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPA43, RRN12, YOR340C, O6271 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P46669 |
-DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK
#8: Protein | Mass: 37732.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPC40, RPA5, RPC5, YPR110C, P8283.18 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07703 |
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#15: Protein | Mass: 16167.860 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPC19, YNL113W, N1937 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P28000 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#10: Protein | Mass: 25117.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB5, RPA7, RPC9, YBR154C, YBR1204 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20434 |
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#11: Protein | Mass: 17931.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPO26, RPB6, YPR187W, P9677.8 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20435 |
#13: Protein | Mass: 16525.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB8, YOR224C, YOR50-14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P20436 |
#14: Protein | Mass: 8290.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPB10, YOR210W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P22139 |
#16: Protein | Mass: 7729.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RPC10, RPB12, YHR143W-A, YHR143BW / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40422 |
-RNA polymerase I-specific transcription initiation factor ... , 4 types, 4 molecules OQSR
#17: Protein | Mass: 72458.258 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RRN3, YKL125W / Production host: Escherichia coli (E. coli) / References: UniProt: P36070 |
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#18: Protein | Mass: 60435.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RRN7, YJL025W, J1273 / Production host: Escherichia coli (E. coli) / References: UniProt: P40992 |
#19: Protein | Mass: 102163.227 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli (E. coli) / References: UniProt: P32786 |
#20: Protein | Mass: 59334.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RRN11, YML043C, YM9827.09C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04712 |
-Non-polymers , 1 types, 1 molecules
#21: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.1075 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction | Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42727 / Symmetry type: POINT |