+Open data
-Basic information
Entry | Database: PDB / ID: 5lmx | |||||||||
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Title | Monomeric RNA polymerase I at 4.9 A resolution | |||||||||
Components |
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Keywords | TRANSCRIPTION / Multi-protein complex / RNA polymerase / Monomeric form | |||||||||
Function / homology | Function and homology information 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 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 / 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 | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Torreira, E. / Louro, J.A. / Gil-Carton, D. / Gallego, O. / Calvo, O. / Fernandez-Tornero, C. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Elife / Year: 2017 Title: The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription. Authors: Eva Torreira / Jaime Alegrio Louro / Irene Pazos / Noelia González-Polo / David Gil-Carton / Ana Garcia Duran / Sébastien Tosi / Oriol Gallego / Olga Calvo / Carlos Fernández-Tornero / Abstract: Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental ...Cell growth requires synthesis of ribosomal RNA by RNA polymerase I (Pol I). Binding of initiation factor Rrn3 activates Pol I, fostering recruitment to ribosomal DNA promoters. This fundamental process must be precisely regulated to satisfy cell needs at any time. We present in vivo evidence that, when growth is arrested by nutrient deprivation, cells induce rapid clearance of Pol I-Rrn3 complexes, followed by the assembly of inactive Pol I homodimers. This dual repressive mechanism reverts upon nutrient addition, thus restoring cell growth. Moreover, Pol I dimers also form after inhibition of either ribosome biogenesis or protein synthesis. Our mutational analysis, based on the electron cryomicroscopy structures of monomeric Pol I alone and in complex with Rrn3, underscores the central role of subunits A43 and A14 in the regulation of differential Pol I complexes assembly and subsequent promoter association. | |||||||||
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 | 5lmx.cif.gz | 806.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lmx.ent.gz | 634.6 KB | Display | PDB format |
PDBx/mmJSON format | 5lmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lmx_validation.pdf.gz | 890 KB | Display | wwPDB validaton report |
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Full document | 5lmx_full_validation.pdf.gz | 989 KB | Display | |
Data in XML | 5lmx_validation.xml.gz | 112.7 KB | Display | |
Data in CIF | 5lmx_validation.cif.gz | 165.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/5lmx ftp://data.pdbj.org/pub/pdb/validation_reports/lm/5lmx | HTTPS FTP |
-Related structure data
Related structure data | 4088MC 4086C 4087C 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 ... , 7 types, 7 molecules ABDGIMN
#1: Protein | Mass: 186676.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P10964, DNA-directed RNA polymerase |
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#2: Protein | Mass: 135910.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P22138, DNA-directed RNA polymerase |
#4: Protein | Mass: 14599.128 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P50106 |
#7: Protein | Mass: 36264.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P46669 |
#9: Protein | Mass: 13676.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32529 |
#13: Protein | Mass: 46721.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: Q01080 |
#14: Protein | Mass: 26933.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P47006 |
-DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK
#3: Protein | Mass: 42850.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40422 |
-Non-polymers , 1 types, 6 molecules
#15: 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
Component | Name: S. cerevisiae RNA polymerase I in the monomeric state / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL | ||||||||||||
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Molecular weight | Value: 0.594 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||
Buffer component |
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Specimen | Conc.: 0.06 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 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 / Nominal magnification: 47000 X / Calibrated magnification: 79096 X / Nominal defocus max: 4200 nm / Nominal defocus min: 1900 nm / Cs: 2 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4 sec. / Electron dose: 68 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1288 |
Image scans | Movie frames/image: 68 / Used frames/image: 1-68 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 190750 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122348 / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 111 / Protocol: RIGID BODY FIT / Space: REAL |