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	Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP.
Journal, issue, pages	Nat Commun, Vol. 12, Issue 1, Page 7236, Year 2021
Publish date	Dec 13, 2021
Authors	Christine E Carbone / Anna B Loveland / Howard B Gamper / Ya-Ming Hou / Gabriel Demo / Andrei A Korostelev /
PubMed Abstract	During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that ...During translation, a conserved GTPase elongation factor-EF-G in bacteria or eEF2 in eukaryotes-translocates tRNA and mRNA through the ribosome. EF-G has been proposed to act as a flexible motor that propels tRNA and mRNA movement, as a rigid pawl that biases unidirectional translocation resulting from ribosome rearrangements, or by various combinations of motor- and pawl-like mechanisms. Using time-resolved cryo-EM, we visualized GTP-catalyzed translocation without inhibitors, capturing elusive structures of ribosome•EF-G intermediates at near-atomic resolution. Prior to translocation, EF-G binds near peptidyl-tRNA, while the rotated 30S subunit stabilizes the EF-G GTPase center. Reverse 30S rotation releases Pi and translocates peptidyl-tRNA and EF-G by ~20 Å. An additional 4-Å translocation initiates EF-G dissociation from a transient ribosome state with highly swiveled 30S head. The structures visualize how nearly rigid EF-G rectifies inherent and spontaneous ribosomal dynamics into tRNA-mRNA translocation, whereas GTP hydrolysis and Pi release drive EF-G dissociation.
External links	Nat Commun / PubMed:34903725 / PubMed Central
Methods	EM (single particle)
Resolution	2.9 - 3.9 Å
Structure data	25405 7ss9 EMDB-25405, PDB-7ss9: Late translocation intermediate with EF-G partially dissociated (Structure V) Method: EM (single particle) / Resolution: 3.9 Å 25407 7ssd EMDB-25407, PDB-7ssd: Mid translocation intermediate with EF-G bound with GDP (Structure IV) Method: EM (single particle) / Resolution: 3.3 Å 25409 7ssl EMDB-25409, PDB-7ssl: Pre translocation intermediate with EF-G bound to GDP and Pi (Structure III) Method: EM (single particle) / Resolution: 3.8 Å 25410 7ssn EMDB-25410, PDB-7ssn: Pre translocation 70S ribosome with *A/P and P/E tRNA (Structure II-B) Method: EM (single particle) / Resolution: 3.2 Å 25411 7sso EMDB-25411, PDB-7sso: Pre translocation 70S ribosome with A/A and P/E tRNA (Structure II-A) Method: EM (single particle) / Resolution: 3.2 Å 25415 7ssw EMDB-25415, PDB-7ssw: Late translocation intermediate with EF-G dissociated (Structure VI) Method: EM (single particle) / Resolution: 3.8 Å 25418 7st2 EMDB-25418, PDB-7st2: Post translocation, non-rotated 70S ribosome with EF-G dissociated (Structure VII) Method: EM (single particle) / Resolution: 2.9 Å 25420 7st6 EMDB-25420, PDB-7st6: Pre translocation, non-rotated 70S ribosome (Structure I) Method: EM (single particle) / Resolution: 3.0 Å 25421 7st7 EMDB-25421, PDB-7st7: Pre translocation intermediate stalled with viomycin and bound with EF-G in a GDP and Pi state (Structure III-vio) Method: EM (single particle) / Resolution**: 3.2 Å
Chemicals	ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying moleculeYM / Guanosine diphosphate ChemComp-PO4: PHOSPHATE ION / Phosphate ChemComp-FME: N-FORMYLMETHIONINE / N-Formylmethionine ChemComp-PRO*: PROLINE / Proline
Source	escherichia coli k-12 (bacteria) escherichia coli 113303 (bacteria) streptomyces californicus (bacteria)
Keywords	RIBOSOME / EF-G / GTP / Translocation / GDP / Hybrid / Classical / RIBOSOME/ANTIBIOTIC / Ribosome-Antibiotic complex / Viomycin