7OTC

Cryo-EM structure of an Escherichia coli 70S ribosome in complex with elongation factor G and the antibiotic Argyrin B


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 1.1 of the entry. See complete history


Literature

The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation.

Wieland, M.Holm, M.Rundlet, E.J.Morici, M.Koller, T.O.Maviza, T.P.Pogorevc, D.Osterman, I.A.Muller, R.Blanchard, S.C.Wilson, D.N.

(2022) Proc Natl Acad Sci U S A 119: e2114214119-e2114214119

  • DOI: https://doi.org/10.1073/pnas.2114214119
  • Primary Citation of Related Structures:  
    7OTC, 7UG7

  • PubMed Abstract: 

    Argyrins are a family of naturally produced octapeptides that display promising antimicrobial activity against Pseudomonas aeruginosa. Argyrin B (ArgB) has been shown to interact with an elongated form of the translation elongation factor G (EF-G), leading to the suggestion that argyrins inhibit protein synthesis by interfering with EF-G binding to the ribosome. Here, using a combination of cryo-electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET), we demonstrate that rather than interfering with ribosome binding, ArgB rapidly and specifically binds EF-G on the ribosome to inhibit intermediate steps of the translocation mechanism. Our data support that ArgB inhibits conformational changes within EF-G after GTP hydrolysis required for translocation and factor dissociation, analogous to the mechanism of fusidic acid, a chemically distinct antibiotic that binds a different region of EF-G. These findings shed light on the mechanism of action of the argyrin-class antibiotics on protein synthesis as well as the nature and importance of rate-limiting, intramolecular conformational events within the EF-G-bound ribosome during late-steps of translocation.


  • Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]226Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth c]206Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]205Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]157Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]106Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]156Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]129Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]127Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth j]99Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]117Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]123Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]115Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth n]101Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]88Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]82Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]80Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]67Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]92Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]86Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth u]70Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth C]271Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Y [auth D]209Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4Z [auth E]201Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth F]177Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth G]176Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13CA [auth J]142Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14DA [auth K]123Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15EA [auth L]144Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16FA [auth M]136Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17GA [auth N]120Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18HA [auth O]116Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19IA [auth P]114Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20JA [auth Q]117Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21KA [auth R]103Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22LA [auth S]110Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23MA [auth T]93Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24NA [auth U]102Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25OA [auth V]94Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27PA [auth W]84Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28QA [auth X]77Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29RA [auth Y]63Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for A0A140N7F5 (Escherichia coli (strain B / BL21-DE3))
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UniProt GroupA0A140N7F5
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30SA [auth Z]58Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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UniProt GroupA0A140N7G4
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31TA [auth 5]67Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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UniProt GroupA0A140SS71
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32UA [auth 0]56Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33VA [auth 1]50Escherichia coli BL21(DE3)Mutation(s): 0 
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Find proteins for A0A140N5Z7 (Escherichia coli (strain B / BL21-DE3))
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UniProt GroupA0A140N5Z7
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34WA [auth 2]46Escherichia coli BL21(DE3)Mutation(s): 0 
UniProt
Find proteins for A0A140NHV0 (Escherichia coli (strain B / BL21-DE3))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35XA [auth 3]64Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36YA [auth 4]38Escherichia coli BL21(DE3)Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor GZA [auth w]704Escherichia coli BL21(DE3)Mutation(s): 2 
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Find proteins for A0A140N7C7 (Escherichia coli (strain B / BL21-DE3))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth a]1,533Escherichia coli BL21(DE3)
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Entity ID: 22
MoleculeChains LengthOrganismImage
23S ribosomal RNAV [auth A]2,903Escherichia coli BL21(DE3)
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Entity ID: 23
MoleculeChains LengthOrganismImage
5S ribosomal RNAW [auth B]120Escherichia coli BL21(DE3)
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1I7 (Subject of Investigation/LOI)
Query on 1I7

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UM [auth w]Argyrin B
C41 H46 N10 O8 S
OVJDNZFLEREPKG-VPMCBBNJSA-N
ATP
Query on ATP

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KD [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GDP
Query on GDP

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TM [auth w]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SPD
Query on SPD

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SD [auth A],
TD [auth A]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
PUT
Query on PUT

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LD [auth A]
MD [auth A]
ND [auth A]
OD [auth A]
PD [auth A]
LD [auth A],
MD [auth A],
ND [auth A],
OD [auth A],
PD [auth A],
QD [auth A],
RD [auth A],
XI [auth A]
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
ZN
Query on ZN

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PM [auth 5],
RM [auth 4]
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],
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],
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],
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],
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],
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],
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 B],
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 B],
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 B],
JB [auth a],
JC [auth a],
JD [auth n],
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 B],
KB [auth a],
KC [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 C],
LB [auth a],
LC [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 C],
MB [auth a],
MC [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 D],
NB [auth a],
NC [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 N],
OB [auth a],
OC [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 Q],
PB [auth a],
PC [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],
QB [auth a],
QC [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 0],
RB [auth a],
RC [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],
SB [auth a],
SC [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 w],
TB [auth a],
TC [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],
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],
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],
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],
XB [auth a],
XC [auth a],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth A],
XJ [auth A],
XK [auth A],
XL [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],
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]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L [auth l]L-PEPTIDE LINKINGC5 H9 N O4 SASP
4D4
Query on 4D4
FA [auth M]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Data collection, Derived calculations, Refinement description