8AM9

Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the elongating ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for translation inhibition by the glycosylated drosocin peptide.

Koller, T.O.Morici, M.Berger, M.Safdari, H.A.Lele, D.S.Beckert, B.Kaur, K.J.Wilson, D.N.

(2023) Nat Chem Biol 19: 1072-1081

  • DOI: https://doi.org/10.1038/s41589-023-01293-7
  • Primary Citation of Related Structures:  
    8AKN, 8AM9, 8ANA

  • PubMed Abstract: 

    The proline-rich antimicrobial peptide (PrAMP) drosocin is produced by Drosophila species to combat bacterial infection. Unlike many PrAMPs, drosocin is O-glycosylated at threonine 11, a post-translation modification that enhances its antimicrobial activity. Here we demonstrate that the O-glycosylation not only influences cellular uptake of the peptide but also interacts with its intracellular target, the ribosome. Cryogenic electron microscopy structures of glycosylated drosocin on the ribosome at 2.0-2.8-Å resolution reveal that the peptide interferes with translation termination by binding within the polypeptide exit tunnel and trapping RF1 on the ribosome, reminiscent of that reported for the PrAMP apidaecin. The glycosylation of drosocin enables multiple interactions with U2609 of the 23S rRNA, leading to conformational changes that break the canonical base pair with A752. Collectively, our study reveals novel molecular insights into the interaction of O-glycosylated drosocin with the ribosome, which provide a structural basis for future development of this class of antimicrobials.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33A [auth 0]55Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 1]46Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35C [auth 2]65Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36D [auth 3]38Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31E [auth 4]70Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth C]241Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3H [auth D]233Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4I [auth E]206Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5J [auth F]167Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, fully modified isoformK [auth G]135Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7L [auth H]179Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8M [auth I]130Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9N [auth J]130Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10O [auth K]103Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11P [auth L]129Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12Q [auth M]124Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13R [auth N]118Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14S [auth O]101Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15T [auth P]89Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16U [auth Q]82Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17V [auth R]84Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18W [auth S]75Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19X [auth T]92Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20Y [auth U]87Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21Z [auth V]71Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth c]273Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3DA [auth d]209Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4EA [auth e]201Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth f]179Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6GA [auth g]177Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth h]149Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13IA [auth i]142Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14JA [auth j]123Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15KA [auth k]144Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16LA [auth l]136Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17MA [auth m]127Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18NA [auth n]117Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19OA [auth o]115Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20PA [auth p]118Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21QA [auth q]103Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22RA [auth r]110Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23SA [auth s]100Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24TA [auth t]104Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25UA [auth u]94Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27VA [auth v]85Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28WA [auth w]78Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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UniProt GroupP0A7M2
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29XA [auth x]63Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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UniProt GroupP0A7M6
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30YA [auth y]59Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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UniProt GroupP0AG51
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32ZA [auth z]57Escherichia coli BW25113Mutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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UniProt GroupP0A7N4
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Drosocin1DB [auth A]19Drosophila melanogasterMutation(s): 0 
Gene Names: Dwil\GK19342Dwil_GK19342
UniProt
Find proteins for P36193 (Drosophila melanogaster)
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UniProt GroupP36193
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P36193-1
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Entity ID: 6
MoleculeChains LengthOrganismImage
16S ribosomal RNAF [auth B]1,534Escherichia coli BW25113
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Entity ID: 27
MoleculeChains LengthOrganismImage
23S ribosomal RNAAA [auth a]2,903Escherichia coli BW25113
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Entity ID: 28
MoleculeChains LengthOrganismImage
5S ribosomal RNABA [auth b]120Escherichia coli BW25113
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth X]12Escherichia coli BW25113
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Entity ID: 54
MoleculeChains LengthOrganismImage
Initiator tRNABB [auth Y]76Escherichia coli BW25113
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Entity ID: 55
MoleculeChains LengthOrganismImage
Leucine tRNACB [auth 8]85Escherichia coli BW25113
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A2G (Subject of Investigation/LOI)
Query on A2G

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NM [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
SPM
Query on SPM

Download Ideal Coordinates CCD File 
FM [auth a]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EB [auth 3],
FB [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth B]
AD [auth B]
AE [auth B]
AF [auth a]
AG [auth a]
AC [auth B],
AD [auth B],
AE [auth B],
AF [auth a],
AG [auth a],
AH [auth a],
AI [auth a],
AJ [auth a],
AK [auth a],
AL [auth a],
AM [auth a],
BC [auth B],
BD [auth B],
BE [auth B],
BF [auth a],
BG [auth a],
BH [auth a],
BI [auth a],
BJ [auth a],
BK [auth a],
BL [auth a],
BM [auth a],
CC [auth B],
CD [auth B],
CE [auth B],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth a],
CJ [auth a],
CK [auth a],
CL [auth a],
CM [auth a],
DC [auth B],
DD [auth B],
DE [auth O],
DF [auth a],
DG [auth a],
DH [auth a],
DI [auth a],
DJ [auth a],
DK [auth a],
DL [auth a],
DM [auth a],
EC [auth B],
ED [auth B],
EE [auth R],
EF [auth a],
EG [auth a],
EH [auth a],
EI [auth a],
EJ [auth a],
EK [auth a],
EL [auth a],
EM [auth a],
FC [auth B],
FD [auth B],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FI [auth a],
FJ [auth a],
FK [auth a],
FL [auth a],
GB [auth B],
GC [auth B],
GD [auth B],
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 B],
HC [auth B],
HD [auth B],
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 B],
IC [auth B],
ID [auth B],
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 B],
JC [auth B],
JD [auth B],
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 B],
KC [auth B],
KD [auth B],
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 b],
LB [auth B],
LC [auth B],
LD [auth B],
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 d],
MB [auth B],
MC [auth B],
MD [auth B],
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 z],
NB [auth B],
NC [auth B],
ND [auth B],
NE [auth a],
NF [auth a],
NG [auth a],
NH [auth a],
NI [auth a],
NJ [auth a],
NK [auth a],
NL [auth a],
OB [auth B],
OC [auth B],
OD [auth B],
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],
PB [auth B],
PC [auth B],
PD [auth B],
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 B],
QC [auth B],
QD [auth B],
QE [auth a],
QF [auth a],
QG [auth a],
QH [auth a],
QI [auth a],
QJ [auth a],
QK [auth a],
QL [auth a],
RB [auth B],
RC [auth B],
RD [auth B],
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 B],
SC [auth B],
SD [auth B],
SE [auth a],
SF [auth a],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
SK [auth a],
SL [auth a],
TB [auth B],
TC [auth B],
TD [auth B],
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 B],
UC [auth B],
UD [auth B],
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 B],
VC [auth B],
VD [auth B],
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 B],
WC [auth B],
WD [auth B],
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 B],
XC [auth B],
XD [auth B],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth a],
XI [auth a],
XJ [auth a],
XK [auth a],
XL [auth a],
YB [auth B],
YC [auth B],
YD [auth B],
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 B],
ZC [auth B],
ZD [auth B],
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  1 Unique
IDChains TypeFormula2D DiagramParent
MEQ
Query on MEQ
DA [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermanyDLR01Kl1820

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-24
    Changes: Data collection
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary