8ANA

Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Drosocin1F [auth A]19Drosophila melanogasterMutation(s): 0 
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Glycosylation
Glycosylation Sites: 1Go to GlyGen: P36193-1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth c]273Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3J [auth d]209Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4K [auth e]201Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5L [auth f]179Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6M [auth g]177Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9N [auth h]149Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13O [auth i]142Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14P [auth j]123Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15Q [auth k]144Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16R [auth l]136Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17S [auth m]127Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18T [auth n]117Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19U [auth o]115Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20V [auth p]118Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21W [auth q]103Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22X [auth r]110Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23Y [auth s]100Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Z [auth t]104Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25AA [auth u]94Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27BA [auth v]85Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28CA [auth w]78Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29DA [auth x]63Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth y]59Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32FA [auth z]57Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 7
MoleculeChains LengthOrganismImage
23S ribosomal RNAG [auth a]2,903Escherichia coli BW25113
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S ribosomal RNAH [auth b]120Escherichia 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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IA [auth A]2-acetamido-2-deoxy-alpha-D-galactopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
SPM
Query on SPM

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JI [auth a]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
ZN
Query on ZN

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GA [auth 3],
HA [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],
BB [auth a],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth a],
BI [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],
DB [auth a],
DC [auth a],
DD [auth a],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth a],
DI [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],
FB [auth a],
FC [auth a],
FD [auth a],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FI [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],
HB [auth a],
HC [auth a],
HD [auth a],
HE [auth a],
HF [auth a],
HG [auth a],
HH [auth a],
HI [auth a],
IB [auth a],
IC [auth a],
ID [auth a],
IE [auth a],
IF [auth a],
IG [auth a],
IH [auth a],
II [auth a],
JA [auth a],
JB [auth a],
JC [auth a],
JD [auth a],
JE [auth a],
JF [auth a],
JG [auth a],
JH [auth a],
KA [auth a],
KB [auth a],
KC [auth a],
KD [auth a],
KE [auth a],
KF [auth a],
KG [auth a],
KH [auth a],
KI [auth b],
LA [auth a],
LB [auth a],
LC [auth a],
LD [auth a],
LE [auth a],
LF [auth a],
LG [auth a],
LH [auth a],
LI [auth b],
MA [auth a],
MB [auth a],
MC [auth a],
MD [auth a],
ME [auth a],
MF [auth a],
MG [auth a],
MH [auth a],
MI [auth b],
NA [auth a],
NB [auth a],
NC [auth a],
ND [auth a],
NE [auth a],
NF [auth a],
NG [auth a],
NH [auth a],
NI [auth b],
OA [auth a],
OB [auth a],
OC [auth a],
OD [auth a],
OE [auth a],
OF [auth a],
OG [auth a],
OH [auth a],
OI [auth b],
PA [auth a],
PB [auth a],
PC [auth a],
PD [auth a],
PE [auth a],
PF [auth a],
PG [auth a],
PH [auth a],
PI [auth c],
QA [auth a],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth a],
QF [auth a],
QG [auth a],
QH [auth a],
QI [auth d],
RA [auth a],
RB [auth a],
RC [auth a],
RD [auth a],
RE [auth a],
RF [auth a],
RG [auth a],
RH [auth a],
RI [auth z],
SA [auth a],
SB [auth a],
SC [auth a],
SD [auth a],
SE [auth a],
SF [auth a],
SG [auth a],
SH [auth a],
TA [auth a],
TB [auth a],
TC [auth a],
TD [auth a],
TE [auth a],
TF [auth a],
TG [auth a],
TH [auth a],
UA [auth a],
UB [auth a],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth a],
UG [auth a],
UH [auth a],
VA [auth a],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth a],
VF [auth a],
VG [auth a],
VH [auth a],
WA [auth a],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth a],
XA [auth a],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth a],
YA [auth a],
YB [auth a],
YC [auth a],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth a],
ZA [auth a],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEQ
Query on MEQ
J [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 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, Refinement description