4AQY image
Deposition Date 2012-04-20
Release Date 2012-07-18
Last Version Date 2023-12-20
Entry Detail
PDB ID:
4AQY
Keywords:
Title:
Structure of ribosome-apramycin complexes
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.50 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 41 21 2
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S RIBOSOMAL RNA
Chain IDs:A
Chain Length:1522
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Chain IDs:B
Chain Length:256
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Chain IDs:C
Chain Length:239
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:D
Chain Length:208
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Chain IDs:E
Chain Length:161
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Chain IDs:F
Chain Length:101
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:G
Chain Length:155
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Chain IDs:H
Chain Length:138
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Chain IDs:I
Chain Length:128
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Chain IDs:J
Chain Length:104
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Chain IDs:K
Chain Length:129
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Chain IDs:L
Chain Length:135
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Chain IDs:M
Chain Length:126
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14
Chain IDs:N
Chain Length:60
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Chain IDs:O
Chain Length:88
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Chain IDs:P
Chain Length:88
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q
Chain Length:104
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Chain IDs:R
Chain Length:88
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Chain IDs:S
Chain Length:92
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Chain IDs:T
Chain Length:106
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN THX
Chain IDs:U (auth: V)
Chain Length:26
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Molecule:5'-R(*UP*UP*CP*AP*AP*AP)-3'
Chain IDs:V (auth: W)
Chain Length:6
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Polymer Type:polyribonucleotide
Molecule:5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3'
Chain IDs:W (auth: Z)
Chain Length:15
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS
Primary Citation
Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin.
Proc.Natl.Acad.Sci.USA 109 10984 ? (2012)
PMID: 22699498 DOI: 10.1073/PNAS.1204073109

Abstact

Aminoglycosides are potent antibacterials, but therapy is compromised by substantial toxicity causing, in particular, irreversible hearing loss. Aminoglycoside ototoxicity occurs both in a sporadic dose-dependent and in a genetically predisposed fashion. We recently have developed a mechanistic concept that postulates a key role for the mitochondrial ribosome (mitoribosome) in aminoglycoside ototoxicity. We now report on the surprising finding that apramycin, a structurally unique aminoglycoside licensed for veterinary use, shows little activity toward eukaryotic ribosomes, including hybrid ribosomes which were genetically engineered to carry the mitoribosomal aminoglycoside-susceptibility A1555G allele. In ex vivo cultures of cochlear explants and in the in vivo guinea pig model of chronic ototoxicity, apramycin causes only little hair cell damage and hearing loss but it is a potent antibacterial with good activity against a range of clinical pathogens, including multidrug-resistant Mycobacterium tuberculosis. These data provide proof of concept that antibacterial activity can be dissected from aminoglycoside ototoxicity. Together with 3D structures of apramycin-ribosome complexes at 3.5-Å resolution, our results provide a conceptual framework for further development of less toxic aminoglycosides by hypothesis-driven chemical synthesis.

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