Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome

This is a large structure.

Summary for 5NDW

Descriptor25S ribosomal RNA, 18S ribosomal RNA, 5S ribosomal RNA, ... (83 entities in total)
Functional Keywordstranslation, ribosome, 40s, 60s, 80s, eukaryote, rna-protein complex, inhibitor, antibiotic, aminoglycoside
Biological sourceSaccharomyces cerevisiae S288c
Cellular locationCytoplasm  Q08745 P0CX47 P48589 P05756 P39516 Q01855 P0CX51 P02407 P0CX55 P07280 P38701 P0C0V8 P0C0W1 P0CX29 P0CX31 Q3E792 P39939 P35997 Q3E7X9 P41057 P0CX33 P0CX45 P14126 P10664 P26321 Q02326 P05737 P17076 P05738 P41805 Q3E757 Q12690 P36105 P05748 P26784 P05740 P0CX49 P0CX82 P0CX23 Q02753 P05749 P0CX41 P04449 P04456 P05743 P0C2H6 P02406 P05747 P14120 P0C2H8 P38061 P05744 P87262 P0CX84 P05745 P49166 P49167 P04650 P0CX86 P0CX27 P0CX25 P32905 P33442 P25443 P05750 P0CX35 P26783 P0CX37 P26786 P0CX39 O13516 P39015 P38011
Ubiquitin: Cytoplasm . 40S ribosomal protein S31: Cytoplasm  P05759
Ubiquitin: Cytoplasm . 60S ribosomal protein L40-A: Cytoplasm  P0CH08
Total number of polymer chains158
Total molecular weight6188106.93
Prokhorova, I.,Djumagulov, M.,Urzhumtsev, A.,Yusupov, M.,Yusupova, G. (deposition date: 2017-03-09, release date: 2017-12-13, Last modification date: 2017-12-27)
Primary citation
Prokhorova, I.,Altman, R.B.,Djumagulov, M.,Shrestha, J.P.,Urzhumtsev, A.,Ferguson, A.,Chang, C.T.,Yusupov, M.,Blanchard, S.C.,Yusupova, G.
Aminoglycoside interactions and impacts on the eukaryotic ribosome.
Proc. Natl. Acad. Sci. U.S.A., 114:E10899-E10908, 2017
PubMed: 29208708 (PDB entries with the same primary citation)
DOI: 10.1073/pnas.1715501114
MImport into Mendeley
Experimental method

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.235161.3%17.3%8.4%0.47MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5ndw
no rotation
Molmil generated image of 5ndw
rotated about x axis by 90°
Molmil generated image of 5ndw
rotated about y axis by 90°