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	Role of aIF5B in archaeal translation initiation.
Journal, issue, pages	Nucleic Acids Res, Vol. 50, Issue 11, Page 6532-6548, Year 2022
Publish date	Jun 24, 2022
Authors	Ramy Kazan / Gabrielle Bourgeois / Christine Lazennec-Schurdevin / Eric Larquet / Yves Mechulam / Pierre-Damien Coureux / Emmanuelle Schmitt /
PubMed Abstract	In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established ...In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 Å resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
External links	Nucleic Acids Res / PubMed:35694843 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.7 - 3.6 Å
Structure data	14579 7zag EMDB-14579, PDB-7zag: Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA,mRNA, aIF1A and the C-terminal domain of aIF5B. Method: EM (single particle) / Resolution: 2.77 Å 14580 7zah EMDB-14580, PDB-7zah: Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA, mRNA, aIF1A and aIF5B Method: EM (single particle) / Resolution: 2.7 Å 14581 7zai EMDB-14581, PDB-7zai: Cryo-EM structure of a Pyrococcus abyssi 30S bound to Met-initiator tRNA, mRNA and aIF1A. Method: EM (single particle) / Resolution: 2.6 Å 14731 7zhg EMDB-14731, PDB-7zhg: High-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop Method: EM (single particle) / Resolution: 2.25 Å 14763 7zki EMDB-14763, PDB-7zki: Cryo-EM structure of aIF1A:aIF5B:Met-tRNAiMet complex from a Pyrococcus abyssi 30S initiation complex Method: EM (single particle) / Resolution: 3.6 Å PDB-7yyp: Structure of aIF5B from Pyrococcus abyssi complexed with GDP Method: X-RAY DIFFRACTION / Resolution: 2.9 Å PDB-7yzn: Structure of C-terminally truncated aIF5B from Pyrococcus abyssi complexed with GTP Method: X-RAY DIFFRACTION / Resolution: 1.7 Å
Chemicals	ChemComp-GDP: GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying moleculeYM / Guanosine diphosphate ChemComp-NO3: NITRATE ION / Nitrate ChemComp-HOH: WATER / Water ChemComp-MG: Unknown entry ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM / Guanosine triphosphate ChemComp-NA: Unknown entry ChemComp-ZN: Unknown entry ChemComp-MET: METHIONINE / Methionine ChemComp-GNP: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate
Source	pyrococcus abyssi ge5 (archaea) pyrococcus abyssi (archaea) escherichia coli (E. coli)
Keywords	TRANSLATION / ribosome / initiator tRNA / initiation factor / eIF5B / IF2 / Initiation complex / translation initiation / small ribosomal subunit / aIF5b