4AQY

Structure of ribosome-apramycin complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Dissociation of Antibacterial Activity and Aminoglycoside Ototoxicity in the 4-Monosubstituted 2-Deoxystreptamine Apramycin.

Matt, T.Ng, C.L.Lang, K.Sha, S.H.Akbergenov, R.Shcherbakov, D.Meyer, M.Duscha, S.Xie, J.Dubbaka, S.R.Perez-Fernandez, D.Vasella, A.Ramakrishnan, V.Schacht, J.Bottger, E.C.

(2012) Proc Natl Acad Sci U S A 109: 10984

  • DOI: https://doi.org/10.1073/pnas.1204073109
  • Primary Citation of Related Structures:  
    4AQY

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2256Thermus thermophilusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3239Thermus thermophilusMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4208Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5161Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6101Thermus thermophilusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7155Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8138Thermus thermophilusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9128Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10104Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11129Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12135Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13126Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1460Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1588Thermus thermophilusMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1688Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17104Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1888Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S1992Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20106Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXU [auth V]26Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNA1,522Thermus thermophilus
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Entity ID: 22
MoleculeChains LengthOrganismImage
5'-R(*UP*UP*CP*AP*AP*AP)-3'V [auth W]6Thermus thermophilus
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Entity ID: 23
MoleculeChains LengthOrganismImage
5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3'W [auth Z]15Thermus thermophilus
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AM2
Query on AM2

Download Ideal Coordinates CCD File 
SH [auth A],
TH [auth A],
UH [auth A],
VH [auth A],
WH [auth A]
APRAMYCIN
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
II [auth N],
YH [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AF [auth A]
BF [auth A]
CF [auth A]
DF [auth A]
EF [auth A]
AF [auth A],
BF [auth A],
CF [auth A],
DF [auth A],
EF [auth A],
KI [auth V],
SE [auth A],
TE [auth A],
UE [auth A],
VE [auth A],
WE [auth A],
XE [auth A],
XH [auth A],
YE [auth A],
ZE [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AG [auth A],
AH [auth A],
AI [auth F],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BG [auth A],
BH [auth A],
BI [auth G],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CG [auth A],
CH [auth A],
CI [auth G],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DG [auth A],
DH [auth A],
DI [auth H],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EG [auth A],
EH [auth A],
EI [auth J],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
FI [auth K],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth L],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth M],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
JI [auth S],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth A],
LI [auth W],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth A],
MI [auth W],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth Z],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SF [auth A],
SG [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TF [auth A],
TG [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UF [auth A],
UG [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VF [auth A],
VG [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WF [auth A],
WG [auth A],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XF [auth A],
XG [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YF [auth A],
YG [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.18α = 90
b = 402.18β = 90
c = 175γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Structure summary
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.4: 2019-05-22
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations, Other
  • Version 1.6: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary