+Open data
-Basic information
Entry | Database: PDB / ID: 5zet | ||||||
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Title | M. smegmatis P/P state 50S ribosomal subunit | ||||||
Components |
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Keywords | RIBOSOME / translating-state / complex | ||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Mishra, S. / Ahmed, T. / Tyagi, A. / Shi, J. / Bhushan, S. | ||||||
Funding support | Singapore, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5zet.cif.gz | 2.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5zet.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 5zet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/5zet ftp://data.pdbj.org/pub/pdb/validation_reports/ze/5zet | HTTPS FTP |
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-Related structure data
Related structure data | 6922MC 6920C 6921C 6923C 6925C 5zebC 5zepC 5zeuC 5zeyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
+50S ribosomal protein ... , 31 types, 31 molecules CDEFGHIJKLMNOPQRSTUVWXYZ1234567
-RNA chain , 2 types, 2 molecules BA
#25: RNA chain | Mass: 38038.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
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#26: RNA chain | Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / References: GenBank: 118168627 |
-Protein/peptide , 1 types, 1 molecules 8
#34: Protein/peptide | Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / References: UniProt: A0QTP4 |
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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 |
-Sample preparation
Component | Name: Translating-state 50S ribosome structure from M.smegmatis Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) / Cellular location: cytoplasm |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Electron dose: 1.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 391837 / Symmetry type: POINT |
Refinement | Highest resolution: 3.2 Å |