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Structure paper

TitleVisualizing translation dynamics at atomic detail inside a bacterial cell.
Journal, issue, pagesNature, Vol. 610, Issue 7930, Page 205-211, Year 2022
Publish dateSep 28, 2022
AuthorsLiang Xue / Swantje Lenz / Maria Zimmermann-Kogadeeva / Dimitry Tegunov / Patrick Cramer / Peer Bork / Juri Rappsilber / Julia Mahamid /
PubMed AbstractTranslation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis to ...Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells. Here we use advances in cryo-electron tomography and sub-tomogram analysis 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. 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.
External linksNature / PubMed:36171285 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution3.4 - 23.0 Å
Structure data

EMDB-13234, PDB-7p6z:
Mycoplasma pneumoniae 70S ribosome in untreated cells
Method: EM (subtomogram averaging) / Resolution: 3.5 Å

EMDB-13272, PDB-7pah:
70S ribosome with P- and E-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.5 Å

EMDB-13273, PDB-7pai:
70S ribosome with P-site tRNA in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 6.7 Å

EMDB-13274, PDB-7paj:
70S ribosome with EF-Tu-tRNA, P- and E-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 7.3 Å

EMDB-13275, PDB-7pak:
70S ribosome with EF-Tu-tRNA and P-site tRNA in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 5.3 Å

EMDB-13276, PDB-7pal:
70S ribosome with A- and P-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 4.7 Å

EMDB-13277, PDB-7pam:
70S ribosome with A*- and P/E-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 6.8 Å

EMDB-13278, PDB-7pan:
70S ribosome with A/P- and P/E-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.7 Å

EMDB-13279, PDB-7pao:
70S ribosome with EF-G, A*- and P/E-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 7.0 Å

EMDB-13280, PDB-7paq:
70S ribosome with EF-G, A/P- and P/E-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 8.9 Å

EMDB-13281, PDB-7par:
70S ribosome with EF-G, ap/P- and pe/E-site tRNAs in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 8.2 Å

EMDB-13282, PDB-7pas:
70S ribosome with P/E-site tRNA in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 16.0 Å

EMDB-13283: 70S ribosome class with unexplained density near P site in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 16.0 Å

EMDB-13284: 70S ribosome with dim 30S subunit in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 23.0 Å

EMDB-13285, PDB-7pat:
free 50S in untreated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.2 Å

EMDB-13286, PDB-7pau:
free 50S in complex with ribosome recycling factor in untreated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 8.3 Å

EMDB-13287: polysome, ribosome pair (conformation 1) in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 12.0 Å

EMDB-13288: polysome, ribosome pair (conformation 2) in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 13.0 Å

EMDB-13289: polysome, ribosome pair (conformation 3) in Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 14.0 Å

EMDB-13410, PDB-7ph9:
70S ribosome with P-site tRNA in chloramphenicol-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 8.7 Å

EMDB-13411, PDB-7pha:
70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenicol-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 8.5 Å

EMDB-13412, PDB-7phb:
70S ribosome with A- and P-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 4.9 Å

EMDB-13413, PDB-7phc:
70S ribosome with A*- and P/E-site tRNAs in chloramphenicol-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.9 Å

EMDB-13414: 70S ribosome with dim 30S subunit in chloramphenicol-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 16.7 Å

EMDB-13431: free 50S in spectinomycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.9 Å

EMDB-13432, PDB-7pi8:
70S ribosome with P-site tRNA in spectinomycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 8.9 Å

EMDB-13433, PDB-7pi9:
70S ribosome with EF-Tu-tRNA and P-site tRNA in spectinomycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 6.3 Å

EMDB-13434, PDB-7pia:
70S ribosome with A/P- and P/E-site tRNAs in spectinomycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 13.6 Å

EMDB-13435, PDB-7pib:
70S ribosome with EF-G, A/P- and P/E-site tRNAs in spectinomycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 4.7 Å

EMDB-13436, PDB-7pic:
70S ribosome with P/E-site tRNA in spectinomycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.1 Å

EMDB-13445, PDB-7pio:
70S ribosome with P-site tRNA in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.5 Å

EMDB-13446, PDB-7pip:
70S ribosome with EF-Tu-tRNA and P-site tRNA in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.3 Å

EMDB-13447, PDB-7piq:
70S ribosome with A- and P-site tRNAs in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 9.7 Å

EMDB-13448, PDB-7pir:
70S ribosome with A*- and P/E-site tRNAs in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 12.1 Å

EMDB-13449, PDB-7pis:
70S ribosome with EF-G, A*- and P/E-site tRNAs in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 15.0 Å

EMDB-13450, PDB-7pit:
70S ribosome with EF-G, A/P- and P/E-site tRNAs in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 5.7 Å

EMDB-13451: 70S ribosome with dim 30S subunit in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 20.7 Å

EMDB-13452: free 50S in pseudouridimycin-treated Mycoplasma pneumoniae cells
Method: EM (subtomogram averaging) / Resolution: 8.7 Å

PDB-7ooc:
Mycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol-treated cells
Method: ELECTRON MICROSCOPY / Resolution: 3.7 Å

PDB-7ood:
Mycoplasma pneumoniae 50S subunit of ribosomes in chloramphenicol-treated cells
Method: ELECTRON MICROSCOPY / Resolution: 3.4 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-CLM:
CHLORAMPHENICOL / antibiotic*YM

ChemComp-SCM:
SPECTINOMYCIN / antibiotic*YM

Source
  • mycoplasma pneumoniae (strain atcc 29342 / m129) (bacteria)
  • mycoplasma pneumoniae m129 (bacteria)
  • mycoplasmoides pneumoniae m129 (bacteria)
KeywordsRIBOSOME / In-cell cryo-electron tomography chloramphenicol-treated sub-tomogram analysis / In-cell cryo-electron tomography / sub-tomogram analysis / TRANSLATION / translation intermediate state / translation termination / chloramphenicol / spectinomycin / pseudouridimycin

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