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- PDB-6tnn: Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tnn | ||||||
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Title | Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA | ||||||
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![]() | RIBOSOMAL PROTEIN / Mini-RNase III / Mini-III / complex / ribosome / 50S / RNA maturation / RNA processing / precursor 23S rRNA / pre-23S rRNA / 23S rRNA / L3 / RNase III-like fold / RNase | ||||||
Function / homology | ![]() positive regulation of rRNA processing / ribonuclease III activity / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / nucleoid / RNA nuclease activity / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding ...positive regulation of rRNA processing / ribonuclease III activity / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / nucleoid / RNA nuclease activity / rRNA processing / large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / DNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.07 Å | ||||||
![]() | Oerum, S. / Dendooven, T. / Gilet, L. / Catala, M. / Degut, C. / Trinquier, A. / Barraud, P. / Luisi, B. / Condon, C. / Tisne, C. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | 1.6 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 10535MC ![]() 6tg6C ![]() 6tgjC ![]() 6tpqC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
+50S ribosomal protein ... , 27 types, 27 molecules bWXYZacdefghijklmnopqrstuvw
-Protein , 1 types, 2 molecules HI
#2: Protein | Mass: 16251.371 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 Gene: mrnC, yazC, BSU00950 / Production host: ![]() ![]() References: UniProt: O31418, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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-RNA chain , 2 types, 2 molecules UV
#3: RNA chain | Mass: 950280.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 467326 |
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#4: RNA chain | Mass: 37420.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: GenBank: 1150402534 |
-Non-polymers , 2 types, 224 molecules ![](data/chem/img/MG.gif)
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#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 |
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Sample preparation
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 23.94 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57683 / Symmetry type: POINT | ||||||||||||
Atomic model building | PDB-ID: 3J3V Accession code: 3J3V / Source name: PDB / Type: experimental model |