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Structure paper

TitleCryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.
Journal, issue, pagesCommun Biol, Vol. 3, Issue 1, Page 58, Year 2020
Publish dateFeb 6, 2020
AuthorsPierre-Damien Coureux / Christine Lazennec-Schurdevin / Sophie Bourcier / Yves Mechulam / Emmanuelle Schmitt /
PubMed AbstractArchaeal 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: ...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.
External linksCommun Biol / PubMed:32029867 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 4.2 Å
Structure data

10320

6sw9

EMDB-10320: IC2A cryo-EM map of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
PDB-6sw9: IC2A model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Method: EM (single particle) / Resolution: 4.2 Å

10322

6swc

EMDB-10322: IC2B cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
PDB-6swc: IC2B model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Method: EM (single particle) / Resolution: 3.3 Å

10323

6swd

EMDB-10323: IC2 body cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
PDB-6swd: IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Method: EM (single particle) / Resolution: 3.2 Å

10324

6swe

EMDB-10324, PDB-6swe:
IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
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

ChemComp-HOH:
WATER / Water

Source
  • pyrococcus abyssi ge5 (archaea)
  • escherichia coli (E. coli)
  • Saccharolobus solfataricus P2 (archaea)
  • pyrococcus abyssi (strain ge5 / orsay) (archaea)
  • saccharolobus solfataricus (strain atcc 35092 / dsm 1617 / jcm 11322 / p2) (archaea)
KeywordsRIBOSOME / Translation initiation / cryo-EM / tRNA / evolution / archaea / rRNA modifications

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