6QUL

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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
  • Structures With Same Primary Citation

  • 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

    Idorsia Pharmaceuticals Ltd, Allschwil, Switzerland. daniel.ritz@idorsia.com.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
273Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
201Escherichia coliMutation(s): 0 
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
179Escherichia coliMutation(s): 0 
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Escherichia coliMutation(s): 0 
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
149Escherichia coliMutation(s): 0 
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
K
142Escherichia coliMutation(s): 0 
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
L
123Escherichia coliMutation(s): 0 
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
M
144Escherichia coliMutation(s): 0 
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
N
136Escherichia coliMutation(s): 0 
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
P
117Escherichia coliMutation(s): 0 
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
Q
115Escherichia coliMutation(s): 0 
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
R
118Escherichia coliMutation(s): 0 
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
S
103Escherichia coliMutation(s): 0 
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
T
110Escherichia coliMutation(s): 0 
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
X
85Escherichia coliMutation(s): 0 
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
Y
78Escherichia coliMutation(s): 0 
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Z
63Escherichia coliMutation(s): 0 
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
b
57Escherichia coliMutation(s): 0 
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
c
55Escherichia coliMutation(s): 0 
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
e
65Escherichia coliMutation(s): 0 
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
f
38Escherichia coliMutation(s): 0 
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q6
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
O
127Escherichia coliMutation(s): 0 
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
U
100Escherichia coliMutation(s): 0 
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
V
104Escherichia coliMutation(s): 0 
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
W
94Escherichia coliMutation(s): 0 
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
a
59Escherichia coliMutation(s): 0 
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
d
46Escherichia coliMutation(s): 0 
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
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Entity ID: 1
MoleculeChainsLengthOrganism
P-site fMet-tRNA(fMet)14Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
23S rRNAA2795Escherichia coli

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Entity ID: 3
MoleculeChainsLengthOrganism
5S rRNAB120Escherichia coli
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JJH
Query on JJH

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

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A
ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
FME
Query on FME

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

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f
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

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