ISDA: 8AKN

Deposition Date 2022-07-30

Release Date 2023-03-08

Last Version Date 2025-03-12

Entry Detail

PDB ID:

8AKN

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Escherichia coli BW25113 (Taxon ID: 679895)
Drosophila melanogaster (Taxon ID: 7227)

Host Organism:

Escherichia coli BL21

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.30 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:A (auth: 0)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7N9 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:B (auth: 1)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:C (auth: 2)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:D (auth: 3)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7Q6 Pfam ID:PF00444

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:E (auth: 4)
Chain Length:70
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7M9 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Drosocin1
Chain IDs:F (auth: A)
Chain Length:19
Number of Molecules:1
Biological Source:Drosophila melanogaster

UniProt ID:P36193

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:G (auth: B)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:H (auth: C)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7V0 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:I (auth: D)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:J (auth: E)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:K (auth: F)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6, fully modified isoform
Gene (Uniprot):rpsF
Chain IDs:L (auth: G)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:M (auth: H)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:N (auth: I)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:O (auth: J)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:P (auth: K)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:Q (auth: L)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:R (auth: M)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:S (auth: N)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:T (auth: O)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:U (auth: P)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADZ4 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:V (auth: Q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:W (auth: R)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:X (auth: S)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:Y (auth: T)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:Z (auth: U)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:AA (auth: V)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P68679 Pfam ID:PF01165

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor RF1
Gene (Uniprot):prfA
Chain IDs:BA (auth: W)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7I0 Pfam ID:PF03462, PF00472

Polymer Type:polyribonucleotide
Molecule:Phenylalanine-tRNA
Chain IDs:CA (auth: X)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:DA (auth: Y)
Chain Length:9
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:Isoleucine-tRNA
Chain IDs:EA (auth: Z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:FA (auth: a)
Chain Length:19
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:GA (auth: b)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:HA (auth: c)
Chain Length:241
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:IA (auth: d)
Chain Length:233
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:JA (auth: e)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:KA (auth: f)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:LA (auth: g)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:MA (auth: h)
Chain Length:179
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:NA (auth: i)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AA10 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:OA (auth: j)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADY3 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:PA (auth: k)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P02413 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:QA (auth: l)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADY7 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:RA (auth: m)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG44 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:SA (auth: n)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0C018 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:TA (auth: o)
Chain Length:115
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7K6 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:UA (auth: p)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7L3 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:VA (auth: q)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:WA (auth: r)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P61175 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:XA (auth: s)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADZ0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:YA (auth: t)
Chain Length:92
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:ZA (auth: u)
Chain Length:87
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:AB (auth: v)
Chain Length:71
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7L8 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:BB (auth: w)
Chain Length:78
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7M2 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:CB (auth: x)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7M6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:DB (auth: y)
Chain Length:9
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG51 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:EB (auth: z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7N4 Pfam ID:PF01783

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MEQ	IA	GLN	modified residue

Ligand Molecules

A2G

SPM

Primary Citation

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.Show

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.

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Disease

Primary Citation of related structures

Abstact

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