6SWD

IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi

Summary for 6SWD

• Entry DOI: 10.2210/pdb6swd/pdb
• EMDB information: 10323
• Descriptor: 16S ribosomal RNA, 30S ribosomal protein S8e, 30S ribosomal protein S11, ... (22 entities in total)
• Functional Keywords: translation initiation, cryo-em, ribosome, trna, evolution, archaea, rrna modifications
• Biological source: Pyrococcus abyssi (strain GE5 / Orsay); More
• Total number of polymer chains: 19
• Total formula weight: 620425.43

Authors

Coureux, P.-D.,Mechulam, Y.,Schmitt, E. (deposition date: 2019-09-20, release date: 2020-02-19, Last modification date: 2025-12-24)

Primary citation

Coureux, P.D.,Lazennec-Schurdevin, C.,Bourcier, S.,Mechulam, Y.,Schmitt, E.
Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Commun Biol, 3:58-58, 2020

PubMed Abstract: Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNA. Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNA complex from Pyrococcus abyssi at 3.2 Å resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.

PubMed: 32029867
DOI: 10.1038/s42003-020-0780-0

Experimental method

ELECTRON MICROSCOPY (3.2 Å)