Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM.
Journal, issue, pages	Nat Commun, Vol. 15, Issue 1, Page 1756, Year 2024
Publish date	Feb 26, 2024
Authors	Timo 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 Abstract	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 ...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 links	Nat Commun / PubMed:38409277 / PubMed Central
Methods	EM (single particle)
Resolution	3.09 - 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 17631 8peg EMDB-17631, PDB-8peg: Escherichia coli paused disome complex (queueing 70S non-rotated closed PRE state) Method: EM (single particle) / Resolution: 3.3 Å 17743 8pkl EMDB-17743, PDB-8pkl: Escherichia coli paused disome complex (leading 70S non-rotated closed PRE state) Method: EM (single particle) / Resolution: 3.09 Å 18875 8r3v EMDB-18875, PDB-8r3v: Escherichia coli paused disome complex (non-rotated disome interface) Method: EM (single particle) / Resolution: 3.28 Å 19054 8rcl EMDB-19054, PDB-8rcl: Escherichia coli paused disome complex (Non-rotated disome interface class 1) Method: EM (single particle) / Resolution: 3.49 Å 19055 8rcm EMDB-19055, PDB-8rcm: Escherichia coli paused disome complex (Non-rotated disome interface class 2) Method: EM (single particle) / Resolution: 3.59 Å 19058 8rcs EMDB-19058, PDB-8rcs: Escherichia coli paused disome complex (Rotated disome interface class 1) Method: EM (single particle) / Resolution: 4.46 Å 19059 8rct 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 moleculeYM / Adenosine triphosphate ChemComp-PUT: 1,4-DIAMINOBUTANE / Putrescine ChemComp-SPD: SPERMIDINE / Spermidine ChemComp-ALA: ALANINE / Alanine ChemComp-HOH*: WATER / Water
Source	escherichia coli (E. coli)
Keywords	RIBOSOME / translation / disome / collision / PURE system / polysome / tranlsation / elongation / pausing