7OOC

Mycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol-treated cells


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Visualizing translation dynamics at atomic detail inside a bacterial cell.

Xue, L.Lenz, S.Zimmermann-Kogadeeva, M.Tegunov, D.Cramer, P.Bork, P.Rappsilber, J.Mahamid, J.

(2022) Nature 610: 205-211

  • DOI: https://doi.org/10.1038/s41586-022-05255-2
  • Primary Citation of Related Structures:  
    7OOC, 7OOD, 7P6Z, 7PAH, 7PAI, 7PAJ, 7PAK, 7PAL, 7PAM, 7PAN, 7PAO, 7PAQ, 7PAR, 7PAS, 7PAT, 7PAU, 7PH9, 7PHA, 7PHB, 7PHC, 7PI8, 7PI9, 7PIA, 7PIB, 7PIC, 7PIO, 7PIP, 7PIQ, 7PIR, 7PIS, 7PIT

  • PubMed Abstract: 

    Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells 1 . Here we use advances in cryo-electron tomography and sub-tomogram analysis 2,3 to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes 4 . By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.


  • Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3A [auth B]273Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P41205 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5B [auth D]219Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50301 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7C [auth F]155Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2D [auth A]294Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9E [auth H]132Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11F [auth J]121Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4G [auth C]205Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20H [auth S]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16I [auth O]94Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12J [auth K]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZK [auth M]61Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10L [auth I]108Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth L]124Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50297 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1586Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19O [auth R]87Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21P [auth T]60Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8Q [auth G]142Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50304 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth Q]104Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75541 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6S [auth E]215Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P75543 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17T [auth P]85Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for Q50309 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 21
MoleculeChains LengthOrganismImage
16S rRNAU [auth 5]1,520Mycoplasmoides pneumoniae M129
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.9
MODEL REFINEMENTPHENIX1.18

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany426290502
Wellcome TrustUnited Kingdom103139
Wellcome TrustUnited Kingdom203149

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-10-12
    Changes: Database references
  • Version 1.2: 2022-10-19
    Changes: Database references
  • Version 1.3: 2024-07-17
    Changes: Data collection, Refinement description