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Yorodumi- EMDB-10535: Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10535 | |||||||||
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Title | Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA | |||||||||
Map data | Mini-RNase III (Mini-III) bound to 50S ribosome with pre-23S rRNA | |||||||||
Sample |
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Keywords | Mini-RNase III / Mini-III / complex / ribosome / 50S / RNA maturation / RNA processing / precursor 23S rRNA / pre-23S rRNA / 23S rRNA / L3 / Ribosomal protein / RNase III-like fold / RNase | |||||||||
Function / homology | Function and homology information positive regulation of rRNA processing / ribonuclease III activity / nucleoid / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA nuclease activity / rRNA processing / large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding ...positive regulation of rRNA processing / ribonuclease III activity / nucleoid / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA nuclease activity / 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 / cytoplasm Similarity search - Function | |||||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) / Bacillus subtilis subsp. subtilis str. 168 / Bacillus subtilis subsp. subtilis str. 168 | |||||||||
Method | single particle reconstruction / Resolution: 3.07 Å | |||||||||
Authors | Oerum S / Dendooven T | |||||||||
Funding support | France, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10535.map.gz | 11.1 MB | EMDB map data format | |
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Header (meta data) | emd-10535-v30.xml emd-10535.xml | 46.3 KB 46.3 KB | Display Display | EMDB header |
Images | emd_10535.png | 80.8 KB | ||
Filedesc metadata | emd-10535.cif.gz | 10.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10535 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10535 | HTTPS FTP |
-Validation report
Summary document | emd_10535_validation.pdf.gz | 403.7 KB | Display | EMDB validaton report |
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Full document | emd_10535_full_validation.pdf.gz | 403.3 KB | Display | |
Data in XML | emd_10535_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_10535_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10535 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10535 | HTTPS FTP |
-Related structure data
Related structure data | 6tnnMC 6tg6C 6tgjC 6tpqC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10535.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mini-RNase III (Mini-III) bound to 50S ribosome with pre-23S rRNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
+Supramolecule #1: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
+Supramolecule #2: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
+Supramolecule #3: Mini-RNase III bound to 50S ribosome with precursor 23S rRNA
+Macromolecule #1: 50S ribosomal protein L10
+Macromolecule #2: Mini-ribonuclease 3
+Macromolecule #5: 50S ribosomal protein L2
+Macromolecule #6: 50S ribosomal protein L3
+Macromolecule #7: 50S ribosomal protein L4
+Macromolecule #8: 50S ribosomal protein L5
+Macromolecule #9: 50S ribosomal protein L6
+Macromolecule #10: 50S ribosomal protein L13
+Macromolecule #11: 50S ribosomal protein L14
+Macromolecule #12: 50S ribosomal protein L15
+Macromolecule #13: 50S ribosomal protein L16
+Macromolecule #14: 50S ribosomal protein L17
+Macromolecule #15: 50S ribosomal protein L18
+Macromolecule #16: 50S ribosomal protein L19
+Macromolecule #17: 50S ribosomal protein L20
+Macromolecule #18: 50S ribosomal protein L21
+Macromolecule #19: 50S ribosomal protein L22
+Macromolecule #20: 50S ribosomal protein L23
+Macromolecule #21: 50S ribosomal protein L24
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L32
+Macromolecule #24: 50S ribosomal protein L33 1
+Macromolecule #25: 50S ribosomal protein L34
+Macromolecule #26: 50S ribosomal protein L35
+Macromolecule #27: 50S ribosomal protein L36
+Macromolecule #28: 50S ribosomal protein L28
+Macromolecule #29: 50S ribosomal protein L29
+Macromolecule #30: 50S ribosomal protein L30
+Macromolecule #3: pre-23S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #31: MAGNESIUM ION
+Macromolecule #32: ZINC ION
-Experimental details
-Structure determination
Processing | single particle reconstruction |
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Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 23.94 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57683 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |