+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6922 | |||||||||
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Title | M. smegmatis P/P state 50S ribosomal subunit | |||||||||
Map data | 50S mask map for translating-state 70S ribosome of M. smegmatis | |||||||||
Sample |
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Function / homology | Function and homology information large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome ...large ribosomal subunit / ribosomal large subunit assembly / transferase activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Mishra S / Ahmed T / Tyagi A / Shi J / Bhushan S | |||||||||
Citation | Journal: Sci Rep / Year: 2018 Title: Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA. Authors: Satabdi Mishra / Tofayel Ahmed / Anu Tyagi / Jian Shi / Shashi Bhushan / Abstract: Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these ...Ribosomes are the dynamic protein synthesis machineries of the cell. They may exist in different functional states in the cell. Therefore, it is essential to have structural information on these different functional states of ribosomes to understand their mechanism of action. Here, we present single particle cryo-EM reconstructions of the Mycobacterium smegmatis 70S ribosomes in the hibernating state (with HPF), trans-translating state (with tmRNA), and the P/P state (with P-tRNA) resolved to 4.1, 12.5, and 3.4 Å, respectively. A comparison of the P/P state with the hibernating state provides possible functional insights about the Mycobacteria-specific helix H54a rRNA segment. Interestingly, densities for all the four OB domains of bS1 protein is visible in the hibernating 70S ribosome displaying the molecular details of bS1-70S interactions. Our structural data shows a Mycobacteria-specific H54a-bS1 interaction which seems to prevent subunit dissociation and degradation during hibernation without the formation of 100S dimer. This indicates a new role of bS1 protein in 70S protection during hibernation in Mycobacteria in addition to its conserved function during translation initiation. | |||||||||
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_6922.map.gz | 21.4 MB | EMDB map data format | |
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Header (meta data) | emd-6922-v30.xml emd-6922.xml | 43.1 KB 43.1 KB | Display Display | EMDB header |
Images | emd_6922.png | 120.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6922 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6922 | HTTPS FTP |
-Validation report
Summary document | emd_6922_validation.pdf.gz | 396.6 KB | Display | EMDB validaton report |
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Full document | emd_6922_full_validation.pdf.gz | 396.2 KB | Display | |
Data in XML | emd_6922_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_6922_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6922 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6922 | HTTPS FTP |
-Related structure data
Related structure data | 5zetMC 6920C 6921C 6923C 6925C 5zebC 5zepC 5zeuC 5zeyC 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_6922.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 50S mask map for translating-state 70S ribosome of M. smegmatis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 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 : Translating-state 50S ribosome structure from M.smegmatis
+Supramolecule #1: Translating-state 50S ribosome structure from M.smegmatis
+Macromolecule #1: 50S ribosomal protein L2
+Macromolecule #2: 50S ribosomal protein L3
+Macromolecule #3: 50S ribosomal protein L4
+Macromolecule #4: 50S ribosomal protein L5
+Macromolecule #5: 50S ribosomal protein L6
+Macromolecule #6: 50S ribosomal protein L9
+Macromolecule #7: 50S ribosomal protein L10
+Macromolecule #8: 50S ribosomal protein L11
+Macromolecule #9: 50S ribosomal protein L13
+Macromolecule #10: 50S ribosomal protein L14
+Macromolecule #11: 50S ribosomal protein L15
+Macromolecule #12: 50S ribosomal protein L16
+Macromolecule #13: 50S ribosomal protein L17
+Macromolecule #14: 50S ribosomal protein L18
+Macromolecule #15: 50S ribosomal protein L19
+Macromolecule #16: 50S ribosomal protein L20
+Macromolecule #17: 50S ribosomal protein L21
+Macromolecule #18: 50S ribosomal protein L22
+Macromolecule #19: 50S ribosomal protein L23
+Macromolecule #20: 50S ribosomal protein L24
+Macromolecule #21: 50S ribosomal protein L25
+Macromolecule #22: 50S ribosomal protein L27
+Macromolecule #23: 50S ribosomal protein L28
+Macromolecule #24: 50S ribosomal protein L29
+Macromolecule #27: 50S ribosomal protein L30
+Macromolecule #28: 50S ribosomal protein L31
+Macromolecule #29: 50S ribosomal protein L32
+Macromolecule #30: 50S ribosomal protein L33 1
+Macromolecule #31: 50S ribosomal protein L34
+Macromolecule #32: 50S ribosomal protein L35
+Macromolecule #33: 50S ribosomal protein L36
+Macromolecule #34: Uncharacterized protein bL37
+Macromolecule #25: P-tRNAfMet
+Macromolecule #26: 23S rRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 1.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 391837 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |