+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6925 | |||||||||
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Title | M. smegmatis Trans-translation state 70S ribosome | |||||||||
Map data | Trans-translating 70S map of M. smegmatis | |||||||||
Sample |
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Keywords | trans-translating state / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | trans-translation / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / RNA binding / cytoplasm / SsrA-binding protein Function and homology information | |||||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) / Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.5 Å | |||||||||
Authors | Mishra S / Ahmed T | |||||||||
Funding support | Singapore, 1 items
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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_6925.map.gz | 22.7 MB | EMDB map data format | |
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Header (meta data) | emd-6925-v30.xml emd-6925.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_6925.png | 92 KB | ||
Filedesc metadata | emd-6925.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6925 | HTTPS FTP |
-Validation report
Summary document | emd_6925_validation.pdf.gz | 393.7 KB | Display | EMDB validaton report |
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Full document | emd_6925_full_validation.pdf.gz | 393.3 KB | Display | |
Data in XML | emd_6925_validation.xml.gz | 7 KB | Display | |
Data in CIF | emd_6925_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6925 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6925 | HTTPS FTP |
-Related structure data
Related structure data | 5zeyMC 6920C 6921C 6922C 6923C 5zebC 5zepC 5zetC 5zeuC 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_6925.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Trans-translating 70S map of M. smegmatis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : tmRNA and SmpB in trans-translating state of M. smegmatis
Entire | Name: tmRNA and SmpB in trans-translating state of M. smegmatis |
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Components |
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-Supramolecule #1: tmRNA and SmpB in trans-translating state of M. smegmatis
Supramolecule | Name: tmRNA and SmpB in trans-translating state of M. smegmatis type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Location in cell: cytoplasm |
Molecular weight | Theoretical: 2.6 MDa |
-Macromolecule #1: tmRNA
Macromolecule | Name: tmRNA / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 119.208492 KDa |
Sequence | String: GGGGCUGAAC GGUUUCGACU UCGAGCAUCG AAUCCAGGGA AGCGUGCCGG UGCAGGCAAG AGACCACCGU AAGCGUCGUU GCAACCAAU UAAGCGCCGA UUCCAAUCAG CGCGACUACG CCCUCGCUGC CUAAGCGACG GCUGGUCUGU CAGACCGGGA G UGCCCUCG ...String: GGGGCUGAAC GGUUUCGACU UCGAGCAUCG AAUCCAGGGA AGCGUGCCGG UGCAGGCAAG AGACCACCGU AAGCGUCGUU GCAACCAAU UAAGCGCCGA UUCCAAUCAG CGCGACUACG CCCUCGCUGC CUAAGCGACG GCUGGUCUGU CAGACCGGGA G UGCCCUCG GCCCGGAUCC UGGCAUCAGC UAGAGGGACC CACCCACGGG UUCGGUCGCG GGACCUGUGG GGACAUCAAA CA GCGACUG GGAUCGUCAU CUCGGCUUGU UCGUGUGACC GGGAGAUCCG AGUAGAGACA UAGCGAACUG CGCACGGAGA AGC CUCGAG GACAUGCCGU AGGACCCGGG UUCAAUUCCC GGCAGCUCCA CCA GENBANK: GENBANK: CP000480.1 |
-Macromolecule #2: A-tRNAfMet
Macromolecule | Name: A-tRNAfMet / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 24.786785 KDa |
Sequence | String: CGCGGGGUGG AGCAGCCUGG UAGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGGUUCAAA UCCGGCCCCC GCAACCA GENBANK: GENBANK: CP016018.1 |
-Macromolecule #3: SsrA-binding protein
Macromolecule | Name: SsrA-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 |
Molecular weight | Theoretical: 18.325039 KDa |
Sequence | String: MTKKSASSNN KVVATNRKAR HNYTILDTYE AGIVLMGTEV KSLREGQASL ADAFATVDDG EIWLRNVHIA EYHHGTWTNH APRRNRKLL LHRKQIDNLI GKIRDGNLTL VPLSIYFTDG KVKVELALAR GKQAHDKRQD LARRDAQREV IRELGRRAKG K I UniProtKB: SsrA-binding protein |
-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
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 391837 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |