8AKN image
Entry Detail
PDB ID:
8AKN
EMDB ID:
Keywords:
Title:
Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the terminating ribosome
Biological Source:
PDB Version:
Deposition Date:
2022-07-30
Release Date:
2023-03-08
Method Details:
Experimental Method:
Resolution:
2.30 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L33
Chain IDs:A (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L34
Chain IDs:B (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L35
Chain IDs:C (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L36
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L31
Chain IDs:E (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:Drosocin1
Chain IDs:F (auth: A)
Chain Length:19
Number of Molecules:1
Biological Source:Drosophila melanogaster
Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:G (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S2
Chain IDs:H (auth: C)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S3
Chain IDs:I (auth: D)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:J (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S5
Chain IDs:K (auth: F)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S6, fully modified isoform
Chain IDs:L (auth: G)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:M (auth: H)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:N (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:O (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S10
Chain IDs:P (auth: K)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S11
Chain IDs:Q (auth: L)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S12
Chain IDs:R (auth: M)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S13
Chain IDs:S (auth: N)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S14
Chain IDs:T (auth: O)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:U (auth: P)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:V (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S17
Chain IDs:W (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:X (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:Y (auth: T)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S20
Chain IDs:Z (auth: U)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:30S ribosomal protein S21
Chain IDs:AA (auth: V)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:Peptide chain release factor RF1
Chain IDs:BA (auth: W)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:Phenylalanine-tRNA
Chain IDs:CA (auth: X)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:mRNA
Chain IDs:DA (auth: Y)
Chain Length:9
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:Isoleucine-tRNA
Chain IDs:EA (auth: Z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:23S ribosomal RNA
Chain IDs:FA (auth: a)
Chain Length:19
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Description:5S ribosomal RNA
Chain IDs:GA (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:HA (auth: c)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L3
Chain IDs:IA (auth: d)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L4
Chain IDs:JA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:KA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:LA (auth: g)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:MA (auth: h)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L13
Chain IDs:NA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:OA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:PA (auth: k)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L16
Chain IDs:QA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:RA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:SA (auth: n)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L19
Chain IDs:TA (auth: o)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:UA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:VA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:WA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L23
Chain IDs:XA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:YA (auth: t)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:ZA (auth: u)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L27
Chain IDs:AB (auth: v)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L28
Chain IDs:BB (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L29
Chain IDs:CB (auth: x)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L30
Chain IDs:DB (auth: y)
Chain Length:9
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polypeptide(L)
Description:50S ribosomal protein L32
Chain IDs:EB (auth: z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MEQ IA GLN modified residue
Primary Citation
Structural basis for translation inhibition by the glycosylated drosocin peptide.
Nat.Chem.Biol. 19 1072 1081 (2023)
PMID: 36997646 DOI: 10.1038/s41589-023-01293-7

Abstact

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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures