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 1.3 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: https://doi.org/10.1038/s41598-019-42155-4
  • Primary Citation of Related Structures:  
    6QUL

  • 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 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

    ETH Zurich, Department of Biology, Zurich, Switzerland.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2D [auth C]273Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3E [auth D]209Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4F [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5G [auth F]179Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6H [auth G]177Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9I [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13J [auth K]142Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14K [auth L]123Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15L [auth M]144Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16M [auth N]136Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17N [auth O]127Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18O [auth P]117Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19P [auth Q]115Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20Q [auth R]118Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21R [auth S]103Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22S [auth T]110Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23T [auth U]100Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24U [auth V]104Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25V [auth W]94Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27W [auth X]85Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28X [auth Y]78Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Y [auth Z]63Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Z [auth a]59Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32AA [auth b]57Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33BA [auth c]55Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34CA [auth d]46Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35DA [auth e]65Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36EA [auth f]38Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
P-site fMet-tRNA(fMet)A [auth 1]4Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S rRNAB [auth A]2,795Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth B]120Escherichia coli
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JJH (Subject of Investigation/LOI)
Query on JJH

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MO [auth A]cadazolid
C29 H29 F2 N3 O8
XWFCFMXQTBGXQW-GOSISDBHSA-N
A
Query on A

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HA [auth A]ADENOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
FME
Query on FME

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FA [auth 1]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
ZN
Query on ZN

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AP [auth f]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth A],
AJ [auth A],
AK [auth A],
AL [auth A],
AM [auth A],
AN [auth A],
AO [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth A],
BM [auth A],
BN [auth A],
BO [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
CL [auth A],
CM [auth A],
CN [auth A],
CO [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
DI [auth A],
DJ [auth A],
DK [auth A],
DL [auth A],
DM [auth A],
DN [auth A],
DO [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
EI [auth A],
EJ [auth A],
EK [auth A],
EL [auth A],
EM [auth A],
EN [auth A],
EO [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 A],
FJ [auth A],
FK [auth A],
FL [auth A],
FM [auth A],
FN [auth A],
FO [auth A],
GA [auth 1],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GJ [auth A],
GK [auth A],
GL [auth A],
GM [auth A],
GN [auth A],
GO [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 A],
HJ [auth A],
HK [auth A],
HL [auth A],
HM [auth A],
HN [auth A],
HO [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth A],
IK [auth A],
IL [auth A],
IM [auth A],
IN [auth A],
IO [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 A],
JJ [auth A],
JK [auth A],
JL [auth A],
JM [auth A],
JN [auth A],
JO [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth A],
KM [auth A],
KN [auth A],
KO [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 A],
LJ [auth A],
LK [auth A],
LL [auth A],
LM [auth A],
LN [auth A],
LO [auth A],
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 A],
MJ [auth A],
MK [auth A],
ML [auth A],
MM [auth A],
MN [auth A],
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 A],
NJ [auth A],
NK [auth A],
NL [auth A],
NM [auth A],
NN [auth A],
NO [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
OL [auth A],
OM [auth A],
ON [auth A],
OO [auth B],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PK [auth A],
PL [auth A],
PM [auth A],
PN [auth A],
PO [auth B],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
QL [auth A],
QM [auth A],
QN [auth A],
QO [auth B],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
RL [auth A],
RM [auth A],
RN [auth A],
RO [auth B],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
SL [auth A],
SM [auth A],
SN [auth A],
SO [auth B],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
TL [auth A],
TM [auth A],
TN [auth A],
TO [auth B],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
UL [auth A],
UM [auth A],
UN [auth A],
UO [auth B],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VK [auth A],
VL [auth A],
VM [auth A],
VN [auth A],
VO [auth B],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth A],
WL [auth A],
WM [auth A],
WN [auth A],
WO [auth C],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth A],
XL [auth A],
XM [auth A],
XN [auth A],
XO [auth O],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth A],
YL [auth A],
YM [auth A],
YN [auth A],
YO [auth R],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
ZK [auth A],
ZL [auth A],
ZM [auth A],
ZN [auth A],
ZO [auth b]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references