5NDG

Crystal structure of geneticin (G418) bound to the yeast 80S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Aminoglycoside interactions and impacts on the eukaryotic ribosome.

Prokhorova, I.Altman, R.B.Djumagulov, M.Shrestha, J.P.Urzhumtsev, A.Ferguson, A.Chang, C.T.Yusupov, M.Blanchard, S.C.Yusupova, G.

(2017) Proc Natl Acad Sci U S A 114: E10899-E10908

  • DOI: 10.1073/pnas.1715501114
  • Primary Citation of Related Structures:  
    5OBM, 5NDG, 5NDJ, 5NDV, 5NDW, 5NDK

  • PubMed Abstract: 
  • Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs) ...

    Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukaryotic translation remain largely unexplored. Here, we use the combination of X-ray crystallography and single-molecule FRET analysis to reveal the interactions of distinct classes of aminoglycosides with the 80S eukaryotic ribosome. Crystal structures of the 80S ribosome in complex with paromomycin, geneticin (G418), gentamicin, and TC007, solved at 3.3- to 3.7-Å resolution, reveal multiple aminoglycoside-binding sites within the large and small subunits, wherein the 6'-hydroxyl substituent in ring I serves as a key determinant of binding to the canonical eukaryotic ribosomal decoding center. Multivalent binding interactions with the human ribosome are also evidenced through their capacity to affect large-scale conformational dynamics within the pretranslocation complex that contribute to multiple aspects of the translation mechanism. The distinct impacts of the aminoglycosides examined suggest that their chemical composition and distinct modes of interaction with the ribosome influence PTC read-through efficiency. These findings provide structural and functional insights into aminoglycoside-induced impacts on the eukaryotic ribosome and implicate pleiotropic mechanisms of action beyond decoding.


    Organizational Affiliation

    Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404 Illkirch, France; marat@igbmc.fr scb2005@med.cornell.edu gula@igbmc.fr.



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40S ribosomal protein S0-A S0s0206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-A S1s1216Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2 S2s2217Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3 S3s3223Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-A S4s4260Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5 S5s5206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-A S6s6236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-A S7s7185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-A S8s8200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-A S9s9185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-A C0c0105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-A C1c1156Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12 C2c2143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13 C3c3150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-A C4c4128Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15 C5c5141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-A C6c6141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-A C7c7136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-A C8c8145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-A C9c9143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20 D0d0107Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-A D1d187Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-A D2d2129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-A D3d3144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-A D4d4134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-A D5d570Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-B D6d697Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-A D7d781Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-A D8d863Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-A D9d953Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-A E0e060Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31 E1e1152Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like protein SRsR318Saccharomyces cerevisiaeMutation(s): 0 
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Suppressor protein STM1 SMsM272Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-A L2l2252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3 L3l3386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-A L4l4361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5 L5l5296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-A L6l6176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-A L7l7223Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-A L8l8233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-A L9l9191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10 M0m0221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-A M1m1169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-A M3m3194Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-A M4m4137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-A M5m5203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-A M6m6197Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-A M7m7184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-A M8m8185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-A M9m9188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-A N0n0172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-A N1n1159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-A N2n298Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-A N3n3135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-A N4n4155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25 N5n5121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-A N6n6126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-A N7n7135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28 N8n8148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29 N9n958Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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60S ribosomal protein L30 O0o0100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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60S ribosomal protein L31-A O1o1109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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60S ribosomal protein L32 O2o2127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
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60S ribosomal protein L33-A O3o3106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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60S ribosomal protein L34-A O4o4112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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60S ribosomal protein L35-A O5o5119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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60S ribosomal protein L36-A O6o699Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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60S ribosomal protein L37-A O7o784Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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60S ribosomal protein L38 O8o877Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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60S ribosomal protein L39 O9o950Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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Ubiquitin-60S ribosomal protein L40 Q0q052Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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60S ribosomal protein L41-A Q1q125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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60S ribosomal protein L42-A Q2q2105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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60S ribosomal protein L43-A Q3q391Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 80
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60S acidic ribosomal protein P0 p0312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S ribosomal RNA2, 61800Saccharomyces cerevisiae
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Entity ID: 36
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25S ribosomal RNA1, 53396Saccharomyces cerevisiae
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Entity ID: 37
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5S ribosomal RNA3, 7121Saccharomyces cerevisiae
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Entity ID: 38
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5.8S ribosomal RNA4, 8158Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GET
Query on GET

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1, 2, 5, 6, n6
GENETICIN
C20 H40 N4 O10
BRZYSWJRSDMWLG-DJWUNRQOSA-N
 Ligand Interaction
ZN
Query on ZN

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D6, D7, D9, E1, O4, O7, Q0, Q2, Q3, d6, d7, d9, e1, o4, o7, q0, q2, q3
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File