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Structure paper

TitleStructure of the mitoribosomal small subunit with streptomycin reveals Fe-S clusters and physiological molecules.
Journal, issue, pagesElife, Vol. 11, Year 2022
Publish dateDec 8, 2022
AuthorsYuzuru Itoh / Vivek Singh / Anas Khawaja / Andreas Naschberger / Minh Duc Nguyen / Joanna Rorbach / Alexey Amunts /
PubMed AbstractThe mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was ...The mitoribosome regulates cellular energy production, and its dysfunction is associated with aging. Inhibition of the mitoribosome can be caused by off-target binding of antimicrobial drugs and was shown to be coupled with a bilateral decreased visual acuity. Previously, we reported mitochondria-specific protein aspects of the mitoribosome, and in this article we present a 2.4-Å resolution structure of the small subunit in a complex with the anti-tuberculosis drug streptomycin that reveals roles of non-protein components. We found iron-sulfur clusters that are coordinated by different mitoribosomal proteins, nicotinamide adenine dinucleotide (NAD) associated with rRNA insertion, and posttranslational modifications. This is the first evidence of inter-protein coordination of iron-sulfur, and the finding of iron-sulfur clusters and NAD as fundamental building blocks of the mitoribosome directly links to mitochondrial disease and aging. We also report details of streptomycin interactions, suggesting that the mitoribosome-bound streptomycin is likely to be in hydrated gem-diol form and can be subjected to other modifications by the cellular milieu. The presented approach of adding antibiotics to cultured cells can be used to define their native structures in a bound form under more physiological conditions, and since streptomycin is a widely used drug for treatment, the newly resolved features can serve as determinants for targeting.
External linksElife / PubMed:36480258 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 2.4 Å
Structure data

13170

7p2e

EMDB-13170, PDB-7p2e:
Human mitochondrial ribosome small subunit in complex with IF3, GMPPMP and streptomycin
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-15542: Human mitochondrial ribosome small subunit in complex with streptomycin
Method: EM (single particle) / Resolution: 2.3 Å

Chemicals

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

ChemComp-SPM:
SPERMINE / Spermine

ChemComp-5I0:
[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium

ChemComp-K:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

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

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM / 5'-Guanylyl imidodiphosphate

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
KeywordsRIBOSOME / Initiation factor 3 / translation / antibiotic / streptomycin

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