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Structure paper

TitleAminoglycoside interactions and impacts on the eukaryotic ribosome.
Journal, issue, pagesProc. Natl. Acad. Sci. U.S.A., Vol. 114, Page E10899-E10908, Year 2017
Publish dateMar 8, 2017 (structure data deposition date)
AuthorsProkhorova, I. / Altman, R.B. / Djumagulov, M. / Shrestha, J.P. / Urzhumtsev, A. / Ferguson, A. / Chang, C.T. / Yusupov, M. / Blanchard, S.C. / Yusupova, G.
External linksProc. Natl. Acad. Sci. U.S.A. / PubMed:29208708
MethodsX-ray diffraction
Resolution2.95 - 3.7 Å
Structure data

PDB-5ndg:
Crystal structure of geneticin (G418) bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.7 Å

PDB-5ndj:
Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)
Method: X-RAY DIFFRACTION / Resolution: 3.15 Å

PDB-5ndk:
Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA
Method: X-RAY DIFFRACTION / Resolution: 2.95 Å

PDB-5ndv:
Crystal structure of Paromomycin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-5ndw:
Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.7 Å

PDB-5obm:
Crystal structure of Gentamicin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-GET:
GENETICIN / antibiotic*YM / G418

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-8UZ:
TC007

ChemComp-PAR:
PAROMOMYCIN / Antimicrobial, medication*YM / Paromomycin

ChemComp-LLL:
(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • thermus thermophilus (strain hb8 / atcc 27634 / dsm 579) (bacteria)
  • escherichia coli (E. coli)
  • saccharomyces cerevisiae (strain atcc 204508 / s288c) (yeast)
  • saccharomyces cerevisiae (strain rm11-1a) (yeast)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsRIBOSOME / translation / 40S / 60S / 80S / eukaryote / RNA-protein complex / inhibitor / antibiotic / aminoglycoside / geneticin / G418 / 30S / 50S / 70S / tRNA / mRNA / bacteria / 3S / paromomycin / aminoglycosides / gentamicin / PTC read-through

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