+Open data
-Basic information
Entry | Database: PDB / ID: 6tpq | ||||||
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Title | RNase M5 bound to 50S ribosome with precursor 5S rRNA | ||||||
Components |
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Keywords | RIBOSOMAL PROTEIN / RNase M5 / M5 / complex / ribosome / 50S / RNA maturation / RNA processing / precursor 5S rRNA / pre-5S rRNA / 5S rRNA / L18 / Toprim domain / RNase | ||||||
Function / homology | Function and homology information ribonuclease M5 / ribonuclease M5 activity / positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding ...ribonuclease M5 / ribonuclease M5 activity / positive regulation of rRNA processing / nucleoid / rRNA processing / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / DNA binding / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.07 Å | ||||||
Authors | Oerum, S. / Dendooven, T. / Gilet, L. / Catala, M. / Degut, C. / Trinquier, A. / Barraud, P. / Luisi, B. / Condon, C. / Tisne, C. | ||||||
Funding support | France, 1items
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Citation | Journal: Mol Cell / Year: 2020 Title: Structures of B. subtilis Maturation RNases Captured on 50S Ribosome with Pre-rRNAs. Authors: Stephanie Oerum / Tom Dendooven / Marjorie Catala / Laetitia Gilet / Clément Dégut / Aude Trinquier / Maxime Bourguet / Pierre Barraud / Sarah Cianferani / Ben F Luisi / Ciarán Condon / Carine Tisné / Abstract: The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ...The pathways for ribosomal RNA (rRNA) maturation diverge greatly among the domains of life. In the Gram-positive model bacterium, Bacillus subtilis, the final maturation steps of the two large ribosomal subunit (50S) rRNAs, 23S and 5S pre-rRNAs, are catalyzed by the double-strand specific ribonucleases (RNases) Mini-RNase III and RNase M5, respectively. Here we present a protocol that allowed us to solve the 3.0 and 3.1 Å resolution cryoelectron microscopy structures of these RNases poised to cleave their pre-rRNA substrates within the B. subtilis 50S particle. These data provide the first structural insights into rRNA maturation in bacteria by revealing how these RNases recognize and process double-stranded pre-rRNA. Our structures further uncover how specific ribosomal proteins act as chaperones to correctly fold the pre-rRNA substrates and, for Mini-III, anchor the RNase to the ribosome. These r-proteins thereby serve a quality-control function in the process from accurate ribosome assembly to rRNA processing. | ||||||
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 | 6tpq.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6tpq.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 6tpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tpq_validation.pdf.gz | 483.7 KB | Display | wwPDB validaton report |
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Full document | 6tpq_full_validation.pdf.gz | 524.9 KB | Display | |
Data in XML | 6tpq_validation.xml.gz | 103.4 KB | Display | |
Data in CIF | 6tpq_validation.cif.gz | 200.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tp/6tpq ftp://data.pdbj.org/pub/pdb/validation_reports/tp/6tpq | HTTPS FTP |
-Related structure data
Related structure data | 10543MC 6tg6C 6tgjC 6tnnC 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
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 20778.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: rnmV, B4109_0079, B4114_0027, D9548_05595, GT94_11730, TGS27_1231 Production host: Escherichia coli (E. coli) / References: UniProt: A0A087LGV4, ribonuclease M5 |
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-RNA chain , 2 types, 2 molecules VU
#2: RNA chain | Mass: 39687.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 1150402534 |
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#4: RNA chain | Mass: 948320.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Bacillus subtilis subsp. subtilis str. 168 (bacteria) References: GenBank: 467326 |
+50S ribosomal protein ... , 27 types, 27 molecules bWXYZacdefghijklmnopqrstuvw
-Non-polymers , 2 types, 222 molecules
#31: Chemical | ChemComp-MG / #32: Chemical | |
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-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) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 23.94 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92799 / Symmetry type: POINT | ||||||||||||
Atomic model building | PDB-ID: 3J3V Accession code: 3J3V / Source name: PDB / Type: experimental model |