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TitleTransient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 1756, Year 2024
Publish dateFeb 26, 2024
AuthorsTimo Flügel / Magdalena Schacherl / Anett Unbehaun / Birgit Schroeer / Marylena Dabrowski / Jörg Bürger / Thorsten Mielke / Thiemo Sprink / Christoph A Diebolder / Yollete V Guillén Schlippe / Christian M T Spahn /
PubMed AbstractStructural studies of translating ribosomes traditionally rely on in vitro assembly and stalling of ribosomes in defined states. To comprehensively visualize bacterial translation, we reactivated ex ...Structural studies of translating ribosomes traditionally rely on in vitro assembly and stalling of ribosomes in defined states. To comprehensively visualize bacterial translation, we reactivated ex vivo-derived E. coli polysomes in the PURE in vitro translation system and analyzed the actively elongating polysomes by cryo-EM. We find that 31% of 70S ribosomes assemble into disome complexes that represent eight distinct functional states including decoding and termination intermediates, and a pre-nucleophilic attack state. The functional diversity of disome complexes together with RNase digest experiments suggests that paused disome complexes transiently form during ongoing elongation. Structural analysis revealed five disome interfaces between leading and queueing ribosomes that undergo rearrangements as the leading ribosome traverses through the elongation cycle. Our findings reveal at the molecular level how bL9's CTD obstructs the factor binding site of queueing ribosomes to thwart harmful collisions and illustrate how translation dynamics reshape inter-ribosomal contacts.
External linksNat Commun / PubMed:38409277 / PubMed Central
MethodsEM (single particle)
Resolution3.09 - 9.11 Å
Structure data

EMDB-17274: Escherichia coli paused disome complex (decoding | rotated PRE)
Method: EM (single particle) / Resolution: 9.06 Å

EMDB-17275: Escherichia coli paused disome complex (decoding | closed non-rot. PRE)
Method: EM (single particle) / Resolution: 8.18 Å

EMDB-17276: Escherichia coli paused disome complex (decoding | POST)
Method: EM (single particle) / Resolution: 9.11 Å

EMDB-17277: Escherichia coli paused disome complex (partially accommodated A-tRNA | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 7.9 Å

EMDB-17278: Escherichia coli paused disome complex (partially accommodated A-tRNA | rotated PRE)
Method: EM (single particle) / Resolution: 8.93 Å

EMDB-17279: Escherichia coli paused disome complex (open non-rotated PRE | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 8.41 Å

EMDB-17280: Escherichia coli paused disome complex (open non-rotated PRE | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 6.95 Å

EMDB-17281: Escherichia coli paused disome complex (open non-rotated PRE | rotated PRE)
Method: EM (single particle) / Resolution: 7.54 Å

EMDB-17282: Escherichia coli paused disome complex (open non-rotated PRE | POST)
Method: EM (single particle) / Resolution: 7.07 Å

EMDB-17283: Escherichia coli paused disome complex (closed non-rotated PRE | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 4.95 Å

EMDB-17284: Escherichia coli paused disome complex (closed non-rotated PRE | rotated PRE)
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-17285: Escherichia coli paused disome complex (closed non-rotated PRE | POST)
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-17286: Escherichia coli paused disome complex (rotated-PRE-1 | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 8.19 Å

EMDB-17288: Escherichia coli paused disome complex (rotated-PRE-1 | rotated PRE)
Method: EM (single particle) / Resolution: 8.62 Å

EMDB-17289: Cryo-EM reconstruction of the E. coli disome complex (rotated-PRE-1 | POST)
Method: EM (single particle) / Resolution: 8.9 Å

EMDB-17291: Escherichia coli paused disome complex (rotated-PRE-2 | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 7.89 Å

EMDB-17431: Escherichia coli paused disome complex (rotated-PRE-2 | rotated PRE)
Method: EM (single particle) / Resolution: 7.58 Å

EMDB-17432: Escherichia coli paused disome complex (rotated-PRE-2 | POST)
Method: EM (single particle) / Resolution: 7.6 Å

EMDB-17433: Escherichia coli paused disome complex (POST | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-17434: Escherichia coli paused disome complex (POST | rotated PRE)
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-17441: Escherichia coli paused disome complex (POST | POST)
Method: EM (single particle) / Resolution: 6.5 Å

EMDB-17442: Escherichia coli paused disome complex (termination | closed non-rotated PRE)
Method: EM (single particle) / Resolution: 6.71 Å

EMDB-17443: Escherichia coli paused disome complex (termination | rotated PRE)
Method: EM (single particle) / Resolution: 7.03 Å

EMDB-17444: Escherichia coli paused disome complex (termination | POST)
Method: EM (single particle) / Resolution: 6.66 Å

EMDB-17631, PDB-8peg:
Escherichia coli paused disome complex (queueing 70S non-rotated closed PRE state)
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-17743, PDB-8pkl:
Escherichia coli paused disome complex (leading 70S non-rotated closed PRE state)
Method: EM (single particle) / Resolution: 3.09 Å

EMDB-18875, PDB-8r3v:
Escherichia coli paused disome complex (non-rotated disome interface)
Method: EM (single particle) / Resolution: 3.28 Å

EMDB-19054, PDB-8rcl:
Escherichia coli paused disome complex (Non-rotated disome interface class 1)
Method: EM (single particle) / Resolution: 3.49 Å

EMDB-19055, PDB-8rcm:
Escherichia coli paused disome complex (Non-rotated disome interface class 2)
Method: EM (single particle) / Resolution: 3.59 Å

EMDB-19058, PDB-8rcs:
Escherichia coli paused disome complex (Rotated disome interface class 1)
Method: EM (single particle) / Resolution: 4.46 Å

EMDB-19059, PDB-8rct:
Escherichia coli paused disome complex (Rotated disome interface class 2)
Method: EM (single particle) / Resolution: 5.32 Å

EMDB-19094: Escherichia coli paused disome complex (local refinement of leading decoding 70S)
Method: EM (single particle) / Resolution: 4.61 Å

EMDB-19095: Escherichia coli paused disome complex (local refinement of leading 70S partially accommodated A-tRNA)
Method: EM (single particle) / Resolution: 4.56 Å

EMDB-19096: Escherichia coli paused disome complex (local refinement of leading 70S rotated PRE-1)
Method: EM (single particle) / Resolution: 3.45 Å

EMDB-19097: Escherichia coli paused disome complex (local refinement of leading 70S rotated PRE-2)
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-19098: Escherichia coli paused disome complex (local refinement of leading 70S open non-rotated PRE)
Method: EM (single particle) / Resolution: 3.79 Å

EMDB-19099: Escherichia coli paused disome complex (local refinement of leading 70S termination)
Method: EM (single particle) / Resolution: 3.82 Å

EMDB-19100: Escherichia coli paused disome complex (local refinement of queueing 70S rotated PRE-2)
Method: EM (single particle) / Resolution: 3.21 Å

EMDB-19101: Escherichia coli paused trisome complex (non-rotated)
Method: EM (single particle) / Resolution: 7.6 Å

EMDB-19102: Escherichia coli paused trisome complex (rotated)
Method: EM (single particle) / Resolution: 7.8 Å

EMDB-19103: Escherichia coli paused disome complex (local refinement of queueing 70S POST)
Method: EM (single particle) / Resolution: 3.21 Å

EMDB-19104: Escherichia coli paused disome complex (local refinement of leading 70S POST)
Method: EM (single particle) / Resolution: 3.21 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-SPD:
SPERMIDINE

ChemComp-ALA:
ALANINE

ChemComp-HOH:
WATER

Source
  • escherichia coli (E. coli)
KeywordsRIBOSOME / translation / disome / collision / PURE system / polysome / tranlsation / elongation / pausing

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