+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6920 | |||||||||
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Title | M. Smegmatis P/P state 70S ribosome structure | |||||||||
Map data | Map of translating-state 70S | |||||||||
Sample |
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Function / homology | Function and homology information large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_6920.map.gz | 24.7 MB | EMDB map data format | |
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Header (meta data) | emd-6920-v30.xml emd-6920.xml | 73.6 KB 73.6 KB | Display Display | EMDB header |
Images | emd_6920.png | 113.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6920 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6920 | HTTPS FTP |
-Validation report
Summary document | emd_6920_validation.pdf.gz | 392.6 KB | Display | EMDB validaton report |
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Full document | emd_6920_full_validation.pdf.gz | 392.1 KB | Display | |
Data in XML | emd_6920_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_6920_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6920 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6920 | HTTPS FTP |
-Related structure data
Related structure data | 5zebMC 6921C 6922C 6923C 6925C 5zepC 5zetC 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_6920.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of translating-state 70S | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 70S ribosome structure from M.smegmatis
+Supramolecule #1: Translating-state 70S ribosome structure from M.smegmatis
+Supramolecule #2: 70S ribosome structure from M.smegmatis
+Supramolecule #3: P-tRNAfMet
+Macromolecule #1: 16S rRNA
+Macromolecule #15: P-tRNAfMet
+Macromolecule #47: 5S rRNA
+Macromolecule #48: 23S rRNA
+Macromolecule #2: 30S ribosomal protein S3
+Macromolecule #3: 30S ribosomal protein S5
+Macromolecule #4: 30S ribosomal protein S7
+Macromolecule #5: 30S ribosomal protein S8
+Macromolecule #6: 30S ribosomal protein S9
+Macromolecule #7: 30S ribosomal protein S10
+Macromolecule #8: 30S ribosomal protein S11
+Macromolecule #9: 30S ribosomal protein S12
+Macromolecule #10: 30S ribosomal protein S15
+Macromolecule #11: 30S ribosomal protein S17
+Macromolecule #12: 30S ribosomal protein S18 2
+Macromolecule #13: 30S ribosomal protein S19
+Macromolecule #14: 30S ribosomal protein S20
+Macromolecule #16: 30S ribosomal protein S14 type Z
+Macromolecule #17: 30S ribosomal protein S2
+Macromolecule #18: 30S ribosomal protein S4
+Macromolecule #19: 30S ribosomal protein S6
+Macromolecule #20: 30S ribosomal protein S13
+Macromolecule #21: 30S ribosomal protein S16
+Macromolecule #22: Conserved domain protein
+Macromolecule #23: 50S ribosomal protein L2
+Macromolecule #24: 50S ribosomal protein L3
+Macromolecule #25: 50S ribosomal protein L4
+Macromolecule #26: 50S ribosomal protein L5
+Macromolecule #27: 50S ribosomal protein L6
+Macromolecule #28: 50S ribosomal protein L9
+Macromolecule #29: 50S ribosomal protein L10
+Macromolecule #30: 50S ribosomal protein L11
+Macromolecule #31: 50S ribosomal protein L13
+Macromolecule #32: 50S ribosomal protein L14
+Macromolecule #33: 50S ribosomal protein L15
+Macromolecule #34: 50S ribosomal protein L16
+Macromolecule #35: 50S ribosomal protein L17
+Macromolecule #36: 50S ribosomal protein L18
+Macromolecule #37: 50S ribosomal protein L19
+Macromolecule #38: 50S ribosomal protein L20
+Macromolecule #39: 50S ribosomal protein L21
+Macromolecule #40: 50S ribosomal protein L22
+Macromolecule #41: 50S ribosomal protein L23
+Macromolecule #42: 50S ribosomal protein L24
+Macromolecule #43: 50S ribosomal protein L25
+Macromolecule #44: 50S ribosomal protein L27
+Macromolecule #45: 50S ribosomal protein L28
+Macromolecule #46: 50S ribosomal protein L29
+Macromolecule #49: 50S ribosomal protein L30
+Macromolecule #50: 50S ribosomal protein L31
+Macromolecule #51: 50S ribosomal protein L32
+Macromolecule #52: 50S ribosomal protein L33 1
+Macromolecule #53: 50S ribosomal protein L34
+Macromolecule #54: 50S ribosomal protein L35
+Macromolecule #55: 50S ribosomal protein L36
+Macromolecule #56: Uncharacterized protein bL37
-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: 3.4 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 |