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Structure paper

TitleStructural basis for the inhibition of the eukaryotic ribosome.
Journal, issue, pagesNature, Vol. 513, Page 517-522, Year 2014
Publish dateJul 22, 2014 (structure data deposition date)
AuthorsGarreau de Loubresse, N. / Prokhorova, I. / Holtkamp, W. / Rodnina, M.V. / Yusupova, G. / Yusupov, M.
External linksNature / PubMed:25209664
MethodsX-ray diffraction
Resolution2.801 - 3.6 Å
Structure data

PDB-4u3m:
Crystal structure of Anisomycin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-4u3n:
Crystal structure of CCA trinucleotide bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-4u3u:
Crystal structure of Cycloheximide bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

PDB-4u4n:
Crystal structure of Edeine bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-4u4o:
Crystal structure of Geneticin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

PDB-4u4q:
Crystal structure of Homoharringtonine bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-4u4r:
Crystal structure of Lactimidomycin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 2.801 Å

PDB-4u4u:
Crystal structure of Lycorine bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-4u4y:
Crystal structure of Pactamycin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-4u4z:
Crystal structure of Phyllanthoside bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

PDB-4u50:
Crystal structure of Verrucarin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-4u51:
Crystal structure of Narciclasine bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-4u52:
Crystal structure of Nagilactone C bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.0 Å

PDB-4u53:
Crystal structure of Deoxynivalenol bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.3 Å

PDB-4u55:
Crystal structure of Cryptopleurine bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

PDB-4u56:
Crystal structure of Blasticidin S bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.45 Å

PDB-4u6f:
Crystal structure of T-2 toxin bound to the yeast 80S ribosome
Method: X-RAY DIFFRACTION / Resolution: 3.1 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-OHX:
osmium (III) hexammine

ChemComp-ZN:
Unknown entry

ChemComp-ANM:
ANISOMYCIN / antibiotic*YM / Anisomycin

ChemComp-A:
ADENOSINE-5'-MONOPHOSPHATE / Adenosine monophosphate

ChemComp-C:
CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate

ChemComp-3HE:
4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione / Cycloheximide

ChemComp-EDE:
EDEINE B

ChemComp-GET:
GENETICIN / antibiotic*YM / G418

ChemComp-HMT:
(3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine / anticancer, alkaloid*YM / Omacetaxine mepesuccinate

ChemComp-3H3:
4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione

ChemComp-3KD:
(1S,2S,12bS,12cS)-2,4,5,7,12b,12c-hexahydro-1H-[1,3]dioxolo[4,5-j]pyrrolo[3,2,1-de]phenanthridine-1,2-diol / alkaloid*YM / Lycorine

ChemComp-PCY:
Pactamycin

ChemComp-3K5:
3-O-acetyl-2-O-(3-O-acetyl-6-deoxy-beta-D-glucopyranosyl)-6-deoxy-1-O-{[(2R,2'S,3a'R,4''S,5''R,6'S,7a'S)-5''-methyl-4''-{[(2E)-3-phenylprop-2-enoyl]oxy}decahydrodispiro[oxirane-2,3'-[1]benzofuran-2',2''-pyran]-6'-yl]carbonyl}-beta-D-glucopyranose

ChemComp-3L2:
(4S,5R,10E,12Z,16R,16aS,17S,18R,19aR,23aR)-4-hydroxy-5,16a,21-trimethyl-4,5,6,7,16,16a,22,23-octahydro-3H,18H,19aH-spiro[16,18-methano[1,6,12]trioxacyclooctadecino[3,4-d]chromene-17,2'-oxirane]-3,9,14-trione / toxin*YM / Verrucarin A

ChemComp-3KF:
(2S,3R,4S,4aR)-2,3,4,7-tetrahydroxy-3,4,4a,5-tetrahydro[1,3]dioxolo[4,5-j]phenanthridin-6(2H)-one / alkaloid*YM / Narciclasine

ChemComp-3J2:
Nagilactone C

ChemComp-3J6:
(3beta,7alpha)-3,7,15-trihydroxy-12,13-epoxytrichothec-9-en-8-one / toxin*YM / Vomitoxin

ChemComp-3K8:
(14aR)-2,3,6-trimethoxy-11,12,13,14,14a,15-hexahydro-9H-dibenzo[f,h]pyrido[1,2-b]isoquinoline

ChemComp-BLS:
BLASTICIDIN S / antibiotic*YM / Blasticidin S

ChemComp-ZBA:
12,13-Epoxytrichothec-9-ene-3,4,8,15-tetrol-4,15-diacetate-8-isovalerate

Source
  • saccharomyces cerevisiae atcc 204508 / s288c (yeast)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsRIBOSOME / translation / 40S / 60S / 80S / eukaryote / RNA-protein complex / inhibitor / antibiotic

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