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Structure paper

TitleMitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 4272, Year 2024
Publish dateMay 20, 2024
AuthorsVivek Singh / Yuzuru Itoh / Samuel Del'Olio / Asem Hassan / Andreas Naschberger / Rasmus Kock Flygaard / Yuko Nobe / Keiichi Izumikawa / Shintaro Aibara / Juni Andréll / Paul C Whitford / Antoni Barrientos / Masato Taoka / Alexey Amunts /
PubMed AbstractThe mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together ...The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNA. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.
External linksNat Commun / PubMed:38769321 / PubMed Central
MethodsEM (single particle)
Resolution2.21 - 2.98 Å
Structure data

13980

7qi4

EMDB-13980: Human mitochondrial ribosome at 2.2 A resolution
PDB-7qi4: Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA)
Method: EM (single particle) / Resolution: 2.21 Å

13981

7qi5

EMDB-13981, PDB-7qi5:
Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution
Method: EM (single particle) / Resolution: 2.63 Å

13982

7qi6

EMDB-13982, PDB-7qi6:
Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution
Method: EM (single particle) / Resolution: 2.98 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

ChemComp-SPM:
SPERMINE

ChemComp-SPD:
SPERMIDINE

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

ChemComp-PUT:
1,4-DIAMINOBUTANE

ChemComp-VAL:
VALINE

ChemComp-HOH:
WATER

Source
  • homo sapiens (human)
KeywordsRIBOSOME / mitochondrial translation / tRNA / mRNA / 2Fe-2S clusters / polyamines / rRNA modifications / post-translation modifications / cryo EM

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