7PAU

free 50S in complex with ribosome recycling factor in untreated Mycoplasma pneumoniae cells


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.30 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
50S ribosomal protein L34A [auth 0]48Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
Find proteins for P78006 (Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35B [auth 1]59Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36C [auth 2]37Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-recycling factorD [auth 7]184Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2E [auth a]287Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3F [auth b]287Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4G [auth c]212Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5H [auth d]180Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6I [auth e]184Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9J [auth f]149Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10K [auth g]161Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11L [auth h]137Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13M [auth i]146Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14N [auth j]122Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15O [auth k]151Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16P [auth l]139Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17Q [auth m]124Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18R [auth n]116Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19S [auth o]119Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20T [auth p]127Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21U [auth q]100Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22V [auth r]159Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23W [auth s]237Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24X [auth t]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Y [auth u]104Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Z [auth v]65Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29AA [auth w]111Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31BA [auth x]97Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32CA [auth y]57Mycoplasmoides pneumoniae M129Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1DA [auth z]53Mycoplasmoides pneumoniae M129Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains LengthOrganismImage
23S ribosomal RNAEA [auth 3]2,907Mycoplasmoides pneumoniae M129
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Entity ID: 32
MoleculeChains LengthOrganismImage
5S ribosomal RNAFA [auth 4]108Mycoplasmoides pneumoniae M129
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.30 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.8
MODEL REFINEMENTPHENIX1.18

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany760067
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