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 1.0 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 

  • DOI: 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 ...

    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

    German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, 38124 Braunschweig, Germany.



Macromolecules

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Entity ID: 3
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50S ribosomal protein L2C [auth K]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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50S ribosomal protein L3D [auth L]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L4E [auth M]201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6F [auth O]177Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L13G [auth R]142Escherichia coli K-12Mutation(s): 0 
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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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50S ribosomal protein L16J [auth U]136Escherichia coli K-12Mutation(s): 0 
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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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50S ribosomal protein L19M [auth X]115Escherichia coli K-12Mutation(s): 0 
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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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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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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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50S ribosomal protein L27T [auth e]85Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L28U [auth f]78Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L29V [auth g]63Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L30W [auth h]59Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L32X [auth i]57Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L33Y [auth j]55Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L34Z [auth k]46Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L35AA [auth l]65Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L36BA [auth m]38Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S2EA [auth D]241Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S3FA [auth E]233Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S4GA [auth F]206Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S5HA [auth G]167Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S6IA [auth H]135Escherichia coli K-12Mutation(s): 0 
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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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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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30S ribosomal protein S12OA [auth q]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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30S ribosomal protein S13PA [auth r]118Escherichia coli K-12Mutation(s): 0 
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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 
Gene Names: rpsOsecCb3165JW3134
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30S ribosomal protein S16SA [auth u]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Find proteins for P0A7T3 (Escherichia coli (strain K12))
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UniProt GroupP0A7T3
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17TA [auth v]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
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UniProt GroupP0AG63
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18UA [auth w]75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Find proteins for P0A7T7 (Escherichia coli (strain K12))
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UniProt GroupP0A7T7
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19VA [auth x]92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20WA [auth y]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21XA [auth 5]71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Myxovalargin BZA [auth z]16Myxococcus fulvusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S ribosomal RNAA [auth I]2,904Escherichia coli K-12
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth J]118Escherichia coli K-12
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Entity ID: 29
MoleculeChainsLengthOrganismImage
P-tRNA fMetCA [auth n]76Escherichia coli K-12
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Entity ID: 30
MoleculeChainsLengthOrganismImage
16S ribosomal RNADA [auth C]1,533Escherichia coli K-12
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Entity ID: 51
MoleculeChainsLengthOrganismImage
messenger RNAYA [auth 6]3Escherichia coli K-12
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FME
Query on FME

Download Ideal Coordinates CCD File 
QG [auth n]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
 Ligand Interaction
SPD
Query on SPD

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

Download Ideal Coordinates CCD File 
PG [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D 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
Entity ID: 52
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002441
Query on PRD_002441
ZA [auth z]Myxovalargin BPeptide-like /  Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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