8B7Y

Cryo-EM structure of the E.coli 70S ribosome in complex with the antibiotic Myxovalargin B.


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 1.1 of the entry. See complete history


Literature

The Myxobacterial Antibiotic Myxovalargin: Biosynthesis, Structural Revision, Total Synthesis, and Molecular Characterization of Ribosomal Inhibition.

Koller, T.O.Scheid, U.Kosel, T.Herrmann, J.Krug, D.Boshoff, H.I.M.Beckert, B.Evans, J.C.Schlemmer, J.Sloan, B.Weiner, D.M.Via, L.E.Moosa, A.Ioerger, T.R.Graf, M.Zinshteyn, B.Abdelshahid, M.Nguyen, F.Arenz, S.Gille, F.Siebke, M.Seedorf, T.Plettenburg, O.Green, R.Warnke, A.L.Ullrich, J.Warrass, R.Barry 3rd, C.E.Warner, D.F.Mizrahi, V.Kirschning, A.Wilson, D.N.Muller, R.

(2023) J Am Chem Soc 145: 851-863

  • DOI: https://doi.org/10.1021/jacs.2c08816
  • Primary Citation of Related Structures:  
    7QQ3, 8B7Y

  • PubMed Abstract: 

    Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum myxobacterial antibiotic myxovalargin and found it to be extremely potent against Mycobacterium tuberculosis . To ensure compound supply for further development, we studied myxovalargin biosynthesis in detail enabling production via fermentation of a native producer. Feeding experiments as well as functional genomics analysis suggested a structural revision, which was eventually corroborated by the development of a concise total synthesis. The ribosome was identified as the molecular target based on resistant mutant sequencing, and a cryo-EM structure revealed that myxovalargin binds within and completely occludes the exit tunnel, consistent with a mode of action to arrest translation during a late stage of translation initiation. These studies open avenues for structure-based scaffold improvement toward development as an antibacterial agent.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland 21205, United States; Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth K]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth L]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth M]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6F [auth O]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13G [auth R]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14H [auth S]123Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L15I [auth T]144Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16J [auth U]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L17K [auth V]127Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18L [auth W]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19M [auth X]115Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20N [auth Y]118Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L21O [auth Z]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
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50S ribosomal protein L22P [auth a]110Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L23Q [auth b]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L24R [auth c]104Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L25S [auth d]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27T [auth e]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28U [auth f]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29V [auth g]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30W [auth h]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32X [auth i]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33Y [auth j]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Z [auth k]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AA [auth l]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36BA [auth m]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2EA [auth D]241Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3FA [auth E]233Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4GA [auth F]206Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5HA [auth G]167Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6IA [auth H]135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7JA [auth N]179Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8KA [auth P]130Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S9LA [auth Q]130Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10MA [auth o]103Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11NA [auth p]129Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12OA [auth q]124Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13PA [auth r]118Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14QA [auth s]101Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S15RA [auth t]89Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16SA [auth u]82Escherichia coli K-12Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17TA [auth v]84Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18UA [auth w]75Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19VA [auth x]92Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20WA [auth y]87Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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UniProt GroupP0A7U7
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21XA [auth 5]71Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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UniProt GroupP68679
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Myxovalargin BZA [auth z]16Myxococcus fulvusMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal RNAA [auth I]2,904Escherichia coli K-12
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth J]118Escherichia coli K-12
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Entity ID: 29
MoleculeChains LengthOrganismImage
P-tRNA fMetCA [auth n]76Escherichia coli K-12
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Entity ID: 30
MoleculeChains LengthOrganismImage
16S ribosomal RNADA [auth C]1,533Escherichia coli K-12
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Entity ID: 51
MoleculeChains LengthOrganismImage
messenger RNAYA [auth 6]3Escherichia coli K-12
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

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QG [auth n]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
SPD
Query on SPD

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AK [auth C],
BK [auth C]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

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PG [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth I]
AC [auth I]
AD [auth I]
AE [auth I]
AF [auth I]
AB [auth I],
AC [auth I],
AD [auth I],
AE [auth I],
AF [auth I],
AG [auth I],
AH [auth C],
AI [auth C],
AJ [auth C],
BB [auth I],
BC [auth I],
BD [auth I],
BE [auth I],
BF [auth I],
BG [auth I],
BH [auth C],
BI [auth C],
BJ [auth C],
CB [auth I],
CC [auth I],
CD [auth I],
CE [auth I],
CF [auth I],
CG [auth I],
CH [auth C],
CI [auth C],
CJ [auth C],
CK [auth G],
DB [auth I],
DC [auth I],
DD [auth I],
DE [auth I],
DF [auth I],
DG [auth I],
DH [auth C],
DI [auth C],
DJ [auth C],
DK [auth q],
EB [auth I],
EC [auth I],
ED [auth I],
EE [auth I],
EF [auth I],
EG [auth I],
EH [auth C],
EI [auth C],
EJ [auth C],
EK [auth s],
FB [auth I],
FC [auth I],
FD [auth I],
FE [auth I],
FF [auth I],
FG [auth I],
FH [auth C],
FI [auth C],
FJ [auth C],
FK [auth 5],
GB [auth I],
GC [auth I],
GD [auth I],
GE [auth I],
GF [auth I],
GG [auth J],
GH [auth C],
GI [auth C],
GJ [auth C],
GK [auth 6],
HB [auth I],
HC [auth I],
HD [auth I],
HE [auth I],
HF [auth I],
HG [auth J],
HH [auth C],
HI [auth C],
HJ [auth C],
IB [auth I],
IC [auth I],
ID [auth I],
IE [auth I],
IF [auth I],
IG [auth K],
IH [auth C],
II [auth C],
IJ [auth C],
JB [auth I],
JC [auth I],
JD [auth I],
JE [auth I],
JF [auth I],
JG [auth T],
JH [auth C],
JI [auth C],
JJ [auth C],
KB [auth I],
KC [auth I],
KD [auth I],
KE [auth I],
KF [auth I],
KG [auth V],
KH [auth C],
KI [auth C],
KJ [auth C],
LB [auth I],
LC [auth I],
LD [auth I],
LE [auth I],
LF [auth I],
LG [auth a],
LH [auth C],
LI [auth C],
LJ [auth C],
MB [auth I],
MC [auth I],
MD [auth I],
ME [auth I],
MF [auth I],
MG [auth a],
MH [auth C],
MI [auth C],
MJ [auth C],
NB [auth I],
NC [auth I],
ND [auth I],
NE [auth I],
NF [auth I],
NG [auth d],
NH [auth C],
NI [auth C],
NJ [auth C],
OB [auth I],
OC [auth I],
OD [auth I],
OE [auth I],
OF [auth I],
OG [auth h],
OH [auth C],
OI [auth C],
OJ [auth C],
PB [auth I],
PC [auth I],
PD [auth I],
PE [auth I],
PF [auth I],
PH [auth C],
PI [auth C],
PJ [auth C],
QB [auth I],
QC [auth I],
QD [auth I],
QE [auth I],
QF [auth I],
QH [auth C],
QI [auth C],
QJ [auth C],
RB [auth I],
RC [auth I],
RD [auth I],
RE [auth I],
RF [auth I],
RG [auth C],
RH [auth C],
RI [auth C],
RJ [auth C],
SB [auth I],
SC [auth I],
SD [auth I],
SE [auth I],
SF [auth I],
SG [auth C],
SH [auth C],
SI [auth C],
SJ [auth C],
TB [auth I],
TC [auth I],
TD [auth I],
TE [auth I],
TF [auth I],
TG [auth C],
TH [auth C],
TI [auth C],
TJ [auth C],
UB [auth I],
UC [auth I],
UD [auth I],
UE [auth I],
UF [auth I],
UG [auth C],
UH [auth C],
UI [auth C],
UJ [auth C],
VB [auth I],
VC [auth I],
VD [auth I],
VE [auth I],
VF [auth I],
VG [auth C],
VH [auth C],
VI [auth C],
VJ [auth C],
WB [auth I],
WC [auth I],
WD [auth I],
WE [auth I],
WF [auth I],
WG [auth C],
WH [auth C],
WI [auth C],
WJ [auth C],
XB [auth I],
XC [auth I],
XD [auth I],
XE [auth I],
XF [auth I],
XG [auth C],
XH [auth C],
XI [auth C],
XJ [auth C],
YB [auth I],
YC [auth I],
YD [auth I],
YE [auth I],
YF [auth I],
YG [auth C],
YH [auth C],
YI [auth C],
YJ [auth C],
ZB [auth I],
ZC [auth I],
ZD [auth I],
ZE [auth I],
ZF [auth I],
ZG [auth C],
ZH [auth C],
ZI [auth C],
ZJ [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
IB9
Query on IB9
ZA [auth z]L-PEPTIDE LINKINGC9 H11 N O3TYR
MAA
Query on MAA
ZA [auth z]L-PEPTIDE LINKINGC4 H9 N O2ALA
RX9
Query on RX9
ZA [auth z]L-PEPTIDE LINKINGC6 H11 N O2ILE
RXL
Query on RXL
ZA [auth z]L-PEPTIDE LINKINGC5 H9 N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
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 & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWI3285/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references