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Yorodumi- PDB-5o60: Structure of the 50S large ribosomal subunit from Mycobacterium s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o60 | |||||||||
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Title | Structure of the 50S large ribosomal subunit from Mycobacterium smegmatis | |||||||||
Components |
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Keywords | RIBOSOME / translation | |||||||||
Function / homology | Function and homology information large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome ...large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium smegmatis str. MC2 155 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Hentschel, J. / Burnside, C. / Mignot, I. / Leibundgut, M. / Boehringer, D. / Ban, N. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: Cell Rep / Year: 2017 Title: The Complete Structure of the Mycobacterium smegmatis 70S Ribosome. Authors: Jendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban / Abstract: The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death ...The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics. | |||||||||
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 | 5o60.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5o60.ent.gz | 1.9 MB | Display | PDB format |
PDBx/mmJSON format | 5o60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o60_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5o60_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5o60_validation.xml.gz | 144 KB | Display | |
Data in CIF | 5o60_validation.cif.gz | 252.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/5o60 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/5o60 | HTTPS FTP |
-Related structure data
Related structure data | 3750MC 3748C 3751C 5o5jC 5o61C 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 ... , 32 types, 32 molecules 3CDEFGHIJKLMNOPQRSTUVWXYZabcdefg
-RNA chain , 3 types, 3 molecules AB2
#2: 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) References: GenBank: 118168627 |
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#3: RNA chain | Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) References: GenBank: 118168627 |
#35: RNA chain | Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tRNA CCA polyribonucleotid, acetylated (Phe) Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria) |
-Non-polymers , 3 types, 413 molecules
#36: Chemical | ChemComp-MG / #37: Chemical | ChemComp-ZN / #38: Chemical | ChemComp-PHE / | |
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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: 50S large ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL |
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Source (natural) | Organism: Mycobacterium smegmatis str. MC2 155 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 96 % |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 100719 X |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Details: FEI EPU data collection |
Image scans | Movie frames/image: 7 |
-Processing
Software | Name: PHENIX / Version: 1.9_1692 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: CTF correction in Relion / Type: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224584 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.18→3.18 Å / SU ML: 0.42 / σ(F): 1.04 / Phase error: 24.53 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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