6QUL

Structure of a bacterial 50S ribosomal subunit in complex with the novel quinoxolidinone antibiotic cadazolid


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of translation inhibition by cadazolid, a novel quinoxolidinone antibiotic.

Scaiola, A.Leibundgut, M.Boehringer, D.Caspers, P.Bur, D.Locher, H.H.Rueedi, G.Ritz, D.

(2019) Sci Rep 9: 5634-5634

  • DOI: 10.1038/s41598-019-42155-4

  • PubMed Abstract: 
  • Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl transferase centre (PTC) of the ribosome and interfering with ...

    Oxazolidinones are synthetic antibiotics used for treatment of infections caused by Gram-positive bacteria. They target the bacterial protein synthesis machinery by binding to the peptidyl transferase centre (PTC) of the ribosome and interfering with the peptidyl transferase reaction. Cadazolid is the first member of quinoxolidinone antibiotics, which are characterized by combining the pharmacophores of oxazolidinones and fluoroquinolones, and it is evaluated for treatment of Clostridium difficile gastrointestinal infections that frequently occur in hospitalized patients. In vitro protein synthesis inhibition by cadazolid was shown in Escherichia coli and Staphylococcus aureus, including an isolate resistant against linezolid, the prototypical oxazolidinone antibiotic. To better understand the mechanism of inhibition, we determined a 3.0 Å cryo-electron microscopy structure of cadazolid bound to the E. coli ribosome in complex with mRNA and initiator tRNA. Here we show that cadazolid binds with its oxazolidinone moiety in a binding pocket in close vicinity of the PTC as observed previously for linezolid, and that it extends its unique fluoroquinolone moiety towards the A-site of the PTC. In this position, the drug inhibits protein synthesis by interfering with the binding of tRNA to the A-site, suggesting that its chemical features also can enable the inhibition of linezolid-resistant strains.


    Organizational Affiliation

    Actelion Pharmaceuticals Ltd, Allschwil, Switzerland.,Polyphor Ltd, Allschwil, Switzerland.,Idorsia Pharmaceuticals Ltd, Allschwil, Switzerland. daniel.ritz@idorsia.com.,Idorsia Pharmaceuticals Ltd, Allschwil, Switzerland.,Actelion Pharmaceuticals Ltd, Allschwil, Switzerland. daniel.ritz@idorsia.com.,ETH Zurich, Department of Biology, Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
115Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
118Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
104Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
78Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
63Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
a
59Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
65Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
Entity ID: 1
MoleculeChainsLengthOrganism
P-site fMet-tRNA(fMet)14Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
23S rRNAA2795Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
5S rRNAB120Escherichia coli
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FME
Query on FME

Download SDF File 
Download CCD File 
1
N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
JJH
Query on JJH

Download SDF File 
Download CCD File 
A
cadazolid
C29 H29 F2 N3 O8
XWFCFMXQTBGXQW-GOSISDBHSA-N
 Ligand Interaction
A
Query on A

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
1, A, b, B, C, O, R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references
  • Version 1.2: 2019-12-18
    Type: Data collection, Other