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Yorodumi- PDB-7y41: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth -
+Open data
-Basic information
Entry | Database: PDB / ID: 7y41 | |||||||||
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Title | Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth | |||||||||
Components |
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Keywords | RIBOSOME / Mycobacterium 50S subunit / Domain IV of 23S rRNA / Log Phase | |||||||||
Function / homology | Function and homology information large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome ...large ribosomal subunit / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Sengupta, J. / Baid, P. | |||||||||
Funding support | India, 2items
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Citation | Journal: Int J Biol Macromol / Year: 2023 Title: Cryo-EM captures a unique conformational rearrangement in 23S rRNA helices of the Mycobacterium 50S subunit. Authors: Priya Baid / Jayati Sengupta / Abstract: Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and ...Structural investigations of the ribosomes isolated from pathogenic and non-pathogenic Mycobacterium species have identified several mycobacteria-specific structural features of ribosomal RNA and proteins. Here, we report structural evidence of a hitherto unknown conformational switch of mycobacterium 23S rRNA helices (H54a and H67-H71). Cryo-electron microscopy (cryo-EM) structures (~3-4 Å) of the M. smegmatis (Msm) log-phase 50S ribosomal subunit revealed conformational variability in H67-H71 region of the 23S rRNA, and manifested that, while H68 possesses the usual stretched conformation in one class of the maps, another one exhibits a bulge-out, fused density of H68-H69 at the inter-subunit surface, indicating an intrinsic dynamics of these rRNA helices. Remarkably, altered conformation of H68 forming a more prominent bulge-out structure at the inter-subunit surface of the 50S subunit due to the conformational rearrangements of 23S rRNA H67-H71 region was clearly visualized in a 3 Å cryo-EM map of the 50S subunit obtained from the stationary phase ribosome dataset. The Msm50S subunit having such bulge-out conformation at the intersubunit surface would be incompatible for associating with the 30S subunit due to its inability to form major inter-subunit bridges. Evidently, availability of active 70S ribosome pool can be modulated by stabilizing either one of the H68 conformation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7y41.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7y41.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 7y41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y41_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7y41_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7y41_validation.xml.gz | 140.2 KB | Display | |
Data in CIF | 7y41_validation.cif.gz | 247.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/7y41 ftp://data.pdbj.org/pub/pdb/validation_reports/y4/7y41 | HTTPS FTP |
-Related structure data
Related structure data | 33599MC 7xamC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein/peptide , 1 types, 1 molecules 3
#1: Protein/peptide | Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria) References: UniProt: A0QTP4 |
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-RNA chain , 2 types, 2 molecules AB
#2: RNA chain | Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Mycolicibacterium smegmatis 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) Mycolicibacterium smegmatis MC2 155 (bacteria) References: GenBank: 118168627 |
+50S ribosomal protein ... , 30 types, 30 molecules CDEFGIJKLMNOPQRSTUVWXYZabcdefg
-Non-polymers , 2 types, 411 molecules
#34: Chemical | ChemComp-MG / #35: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | Y |
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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: Mycobacterium smegmatis 50S ribosomal subunit from Log Phase of growth Type: RIBOSOME / Entity ID: #1-#33 / Source: NATURAL |
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Molecular weight | Value: 1.8 MDa / Experimental value: YES |
Source (natural) | Organism: Mycolicibacterium smegmatis MC2 155 (bacteria) |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3300 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29350 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5O60 Accession code: 5O60 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 4.1 Å |