+Open data
-Basic information
Entry | Database: PDB / ID: 7aoe | |||||||||
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Title | Schizosaccharomyces pombe RNA polymerase I (elongation complex) | |||||||||
Components |
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Keywords | TRANSCRIPTION | |||||||||
Function / homology | Function and homology information RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / 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 Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / mRNA Capping ...RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / 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 Initiation And Promoter Clearance / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / mRNA Capping / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase I Promoter Escape / Formation of the Early Elongation Complex / Formation of TC-NER Pre-Incision Complex / RNA Polymerase II Transcription Elongation / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA-templated transcription elongation / termination of RNA polymerase I transcription / RNA polymerase III activity / RNA polymerase I activity / transcription initiation at RNA polymerase I promoter / tRNA transcription by RNA polymerase III / transcription elongation by RNA polymerase I / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / transcription initiation at RNA polymerase II promoter / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nucleolus / DNA binding / zinc ion binding / metal ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Heiss, F. / Daiss, J. / Becker, P. / Engel, C. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Commun / Year: 2021 Title: Conserved strategies of RNA polymerase I hibernation and activation. Authors: Florian B Heiss / Julia L Daiß / Philipp Becker / Christoph Engel / Abstract: RNA polymerase (Pol) I transcribes the ribosomal RNA precursor in all eukaryotes. The mechanisms 'activation by cleft contraction' and 'hibernation by dimerization' are unique to the regulation of ...RNA polymerase (Pol) I transcribes the ribosomal RNA precursor in all eukaryotes. The mechanisms 'activation by cleft contraction' and 'hibernation by dimerization' are unique to the regulation of this enzyme, but structure-function analysis is limited to baker's yeast. To understand whether regulation by such strategies is specific to this model organism or conserved among species, we solve three cryo-EM structures of Pol I from Schizosaccharomyces pombe in different functional states. Comparative analysis of structural models derived from high-resolution reconstructions shows that activation is accomplished by a conserved contraction of the active center cleft. In contrast to current beliefs, we find that dimerization of the S. pombe polymerase is also possible. This dimerization is achieved independent of the 'connector' domain but relies on two previously undescribed interfaces. Our analyses highlight the divergent nature of Pol I transcription systems from their counterparts and suggest conservation of regulatory mechanisms among organisms. | |||||||||
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 | 7aoe.cif.gz | 727.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aoe.ent.gz | 573.4 KB | Display | PDB format |
PDBx/mmJSON format | 7aoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/7aoe ftp://data.pdbj.org/pub/pdb/validation_reports/ao/7aoe | HTTPS FTP |
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-Related structure data
Related structure data | 11842MC 7aocC 7aodC 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-directed RNA polymerase I subunit ... , 4 types, 4 molecules ADGI
#1: Protein | Mass: 189489.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: P15398, DNA-directed RNA polymerase |
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#4: Protein | Mass: 17008.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: Q9P7P1 |
#7: Protein | Mass: 19406.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: O43036 |
#9: Protein | Mass: 13127.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: O94703 |
-DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK
#3: Protein | Mass: 39205.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: O94616 |
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#11: Protein | Mass: 13734.478 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: rpc19, rpa17, SPAC1687.01, SPAPYUL23.01 / Production host: Schizosaccharomyces pombe (fission yeast) / References: UniProt: Q09177 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#5: Protein | Mass: 23954.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: Q09191 |
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#6: Protein | Mass: 15742.497 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: P36595 |
#8: Protein | Mass: 14317.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: Q92399 |
#10: Protein | Mass: 8286.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: O13877 |
#12: Protein | Mass: 7216.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: P48011 |
-DNA chain , 2 types, 2 molecules UT
#13: DNA chain | Mass: 12085.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#14: DNA chain | Mass: 11942.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Protein / RNA chain / Non-polymers , 3 types, 8 molecules BR
#15: RNA chain | Mass: 6383.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#16: Chemical | ChemComp-ZN / #2: Protein | | Mass: 131854.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / References: UniProt: Q9P7X8, DNA-directed RNA polymerase |
-Details
Has ligand of interest | N |
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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: 7.8 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 88.28 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61954 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.46 Å2 | ||||||||||||||||||||||||
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