7A0R

50S Deinococcus radiodurans ribosome bounded with mycinamicin I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Ribosome-binding and anti-microbial studies of the mycinamicins, 16-membered macrolide antibiotics from Micromonospora griseorubida.

Breiner-Goldstein, E.Eyal, Z.Matzov, D.Halfon, Y.Cimicata, G.Baum, M.Rokney, A.Ezernitchi, A.V.Lowell, A.N.Schmidt, J.J.Rozenberg, H.Zimmerman, E.Bashan, A.Valinsky, L.Anzai, Y.Sherman, D.H.Yonath, A.

(2021) Nucleic Acids Res 49: 9560-9573

  • DOI: https://doi.org/10.1093/nar/gkab684
  • Primary Citation of Related Structures:  
    7A0R, 7A0S, 7A18

  • PubMed Abstract: 

    Macrolides have been effective clinical antibiotics for over 70 years. They inhibit protein biosynthesis in bacterial pathogens by narrowing the nascent protein exit tunnel in the ribosome. The macrolide class of natural products consist of a macrolactone ring linked to one or more sugar molecules. Most of the macrolides used currently are semi-synthetic erythromycin derivatives, composed of a 14- or 15-membered macrolactone ring. Rapidly emerging resistance in bacterial pathogens is among the most urgent global health challenges, which render many antibiotics ineffective, including next-generation macrolides. To address this threat and advance a longer-term plan for developing new antibiotics, we demonstrate how 16-membered macrolides overcome erythromycin resistance in clinically isolated Staphylococcus aureus strains. By determining the structures of complexes of the large ribosomal subunit of Deinococcus radiodurans (D50S) with these 16-membered selected macrolides, and performing anti-microbial studies, we identified resistance mechanisms they may overcome. This new information provides important insights toward the rational design of therapeutics that are effective against drug resistant human pathogens.


  • Organizational Affiliation

    Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 760001, Israel.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]271Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth B]206Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]197Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]177Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]171Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth G]143Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXY1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth H]134Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth I]137Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSK9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth J]136Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth K]116Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSJ5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth L]104Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth M]113Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RWB4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth N]117Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth O]98Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth P]128Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth Q]93Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth R]110Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25T [auth S]175Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27U [auth T]74Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28V [auth U]74Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RRG8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth V]61Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth W]55Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSL0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Y [auth Z]58Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33Z [auth 1]49Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AA [auth 2]47Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BA [auth 3]63Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
UniProt
Find proteins for Q9RSW6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (2730-MER)A [auth X]2,877Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (120-MER)B [auth Y]120Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QTZ (Subject of Investigation/LOI)
Query on QTZ

Download Ideal Coordinates CCD File 
CA [auth X]mycinamicin II
C37 H61 N O13
WWIDEZOUVSJVHS-LWQULZAOSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth X]
AC [auth X]
AD [auth X]
AE [auth X]
AF [auth X]
AB [auth X],
AC [auth X],
AD [auth X],
AE [auth X],
AF [auth X],
AG [auth X],
AH [auth X],
AI [auth X],
AJ [auth X],
AK [auth X],
AL [auth X],
AM [auth X],
AN [auth Y],
BB [auth X],
BC [auth X],
BD [auth X],
BE [auth X],
BF [auth X],
BG [auth X],
BH [auth X],
BI [auth X],
BJ [auth X],
BK [auth X],
BL [auth X],
BM [auth X],
BN [auth A],
CB [auth X],
CC [auth X],
CD [auth X],
CE [auth X],
CF [auth X],
CG [auth X],
CH [auth X],
CI [auth X],
CJ [auth X],
CK [auth X],
CL [auth X],
CM [auth X],
CN [auth A],
DA [auth X],
DB [auth X],
DC [auth X],
DD [auth X],
DE [auth X],
DF [auth X],
DG [auth X],
DH [auth X],
DI [auth X],
DJ [auth X],
DK [auth X],
DL [auth X],
DM [auth X],
DN [auth A],
EA [auth X],
EB [auth X],
EC [auth X],
ED [auth X],
EE [auth X],
EF [auth X],
EG [auth X],
EH [auth X],
EI [auth X],
EJ [auth X],
EK [auth X],
EL [auth X],
EM [auth X],
EN [auth I],
FA [auth X],
FB [auth X],
FC [auth X],
FD [auth X],
FE [auth X],
FF [auth X],
FG [auth X],
FH [auth X],
FI [auth X],
FJ [auth X],
FK [auth X],
FL [auth X],
FM [auth X],
FN [auth J],
GA [auth X],
GB [auth X],
GC [auth X],
GD [auth X],
GE [auth X],
GF [auth X],
GG [auth X],
GH [auth X],
GI [auth X],
GJ [auth X],
GK [auth X],
GL [auth X],
GM [auth X],
GN [auth J],
HA [auth X],
HB [auth X],
HC [auth X],
HD [auth X],
HE [auth X],
HF [auth X],
HG [auth X],
HH [auth X],
HI [auth X],
HJ [auth X],
HK [auth X],
HL [auth X],
HM [auth X],
HN [auth K],
IA [auth X],
IB [auth X],
IC [auth X],
ID [auth X],
IE [auth X],
IF [auth X],
IG [auth X],
IH [auth X],
II [auth X],
IJ [auth X],
IK [auth X],
IL [auth X],
IM [auth X],
IN [auth O],
JA [auth X],
JB [auth X],
JC [auth X],
JD [auth X],
JE [auth X],
JF [auth X],
JG [auth X],
JH [auth X],
JI [auth X],
JJ [auth X],
JK [auth X],
JL [auth X],
JM [auth X],
JN [auth 2],
KA [auth X],
KB [auth X],
KC [auth X],
KD [auth X],
KE [auth X],
KF [auth X],
KG [auth X],
KH [auth X],
KI [auth X],
KJ [auth X],
KK [auth X],
KL [auth X],
KM [auth X],
LA [auth X],
LB [auth X],
LC [auth X],
LD [auth X],
LE [auth X],
LF [auth X],
LG [auth X],
LH [auth X],
LI [auth X],
LJ [auth X],
LK [auth X],
LL [auth X],
LM [auth Y],
MA [auth X],
MB [auth X],
MC [auth X],
MD [auth X],
ME [auth X],
MF [auth X],
MG [auth X],
MH [auth X],
MI [auth X],
MJ [auth X],
MK [auth X],
ML [auth X],
MM [auth Y],
NA [auth X],
NB [auth X],
NC [auth X],
ND [auth X],
NE [auth X],
NF [auth X],
NG [auth X],
NH [auth X],
NI [auth X],
NJ [auth X],
NK [auth X],
NL [auth X],
NM [auth Y],
OA [auth X],
OB [auth X],
OC [auth X],
OD [auth X],
OE [auth X],
OF [auth X],
OG [auth X],
OH [auth X],
OI [auth X],
OJ [auth X],
OK [auth X],
OL [auth X],
OM [auth Y],
PA [auth X],
PB [auth X],
PC [auth X],
PD [auth X],
PE [auth X],
PF [auth X],
PG [auth X],
PH [auth X],
PI [auth X],
PJ [auth X],
PK [auth X],
PL [auth X],
PM [auth Y],
QA [auth X],
QB [auth X],
QC [auth X],
QD [auth X],
QE [auth X],
QF [auth X],
QG [auth X],
QH [auth X],
QI [auth X],
QJ [auth X],
QK [auth X],
QL [auth X],
QM [auth Y],
RA [auth X],
RB [auth X],
RC [auth X],
RD [auth X],
RE [auth X],
RF [auth X],
RG [auth X],
RH [auth X],
RI [auth X],
RJ [auth X],
RK [auth X],
RL [auth X],
RM [auth Y],
SA [auth X],
SB [auth X],
SC [auth X],
SD [auth X],
SE [auth X],
SF [auth X],
SG [auth X],
SH [auth X],
SI [auth X],
SJ [auth X],
SK [auth X],
SL [auth X],
SM [auth Y],
TA [auth X],
TB [auth X],
TC [auth X],
TD [auth X],
TE [auth X],
TF [auth X],
TG [auth X],
TH [auth X],
TI [auth X],
TJ [auth X],
TK [auth X],
TL [auth X],
TM [auth Y],
UA [auth X],
UB [auth X],
UC [auth X],
UD [auth X],
UE [auth X],
UF [auth X],
UG [auth X],
UH [auth X],
UI [auth X],
UJ [auth X],
UK [auth X],
UL [auth X],
UM [auth Y],
VA [auth X],
VB [auth X],
VC [auth X],
VD [auth X],
VE [auth X],
VF [auth X],
VG [auth X],
VH [auth X],
VI [auth X],
VJ [auth X],
VK [auth X],
VL [auth X],
VM [auth Y],
WA [auth X],
WB [auth X],
WC [auth X],
WD [auth X],
WE [auth X],
WF [auth X],
WG [auth X],
WH [auth X],
WI [auth X],
WJ [auth X],
WK [auth X],
WL [auth X],
WM [auth Y],
XA [auth X],
XB [auth X],
XC [auth X],
XD [auth X],
XE [auth X],
XF [auth X],
XG [auth X],
XH [auth X],
XI [auth X],
XJ [auth X],
XK [auth X],
XL [auth X],
XM [auth Y],
YA [auth X],
YB [auth X],
YC [auth X],
YD [auth X],
YE [auth X],
YF [auth X],
YG [auth X],
YH [auth X],
YI [auth X],
YJ [auth X],
YK [auth X],
YL [auth X],
YM [auth Y],
ZA [auth X],
ZB [auth X],
ZC [auth X],
ZD [auth X],
ZE [auth X],
ZF [auth X],
ZG [auth X],
ZH [auth X],
ZI [auth X],
ZJ [auth X],
ZK [auth X],
ZL [auth X],
ZM [auth Y]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.484α = 90
b = 408.933β = 90
c = 697.322γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)322581
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118101

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 1.1: 2022-04-27
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description