ISDA: 9TEW

Deposition Date 2025-11-26

Release Date 2026-05-13

Last Version Date 2026-07-22

Entry Detail

PDB ID:

9TEW

Keywords:

ANTIBIOTIC

Title:

DalDro bound to the initiating Escherichia coli 70S ribosome

Biological Source:

Source Organism(s):

Drosophila (Taxon ID: 7215)
Escherichia coli BW25113 (Taxon ID: 679895)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

2.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmG
Chain IDs:H (auth: 0)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7N9 Pfam ID:PF00471

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmH
Chain IDs:I (auth: 1)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7P5 Pfam ID:PF00468

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmI
Chain IDs:J (auth: 2)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7Q1 Pfam ID:PF01632

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmJ
Chain IDs:E (auth: 3)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7Q6 Pfam ID:PF00444

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmE
Chain IDs:D (auth: 4)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7M9 Pfam ID:PF01197

Polymer Type:polypeptide(L)
Molecule:DalDro
Chain IDs:CB (auth: 8)
Chain Length:0
Number of Molecules:1
Biological Source:Drosophila

Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:G (auth: A)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:K (auth: B)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7V0 Pfam ID:PF00318

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsC
Chain IDs:L (auth: C)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsD
Chain IDs:M (auth: D)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsE
Chain IDs:N (auth: E)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6, ful
Gene (Uniprot):rpsF
Chain IDs:O (auth: F)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P02358 Pfam ID:PF01250

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:ZA (auth: G)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P02359 Pfam ID:PF00177

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsH
Chain IDs:P (auth: H)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7W7 Pfam ID:PF00410

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsI
Chain IDs:Q (auth: I)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7X3 Pfam ID:PF00380

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsJ
Chain IDs:AB (auth: J)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7R5 Pfam ID:PF00338

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsK
Chain IDs:A (auth: K)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7R9 Pfam ID:PF00411

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsL
Chain IDs:B (auth: L)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7S3 Pfam ID:PF00164

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsM
Chain IDs:R (auth: M)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7S9 Pfam ID:PF00416

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsN
Chain IDs:S (auth: N)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG59 Pfam ID:PF00253

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsO
Chain IDs:T (auth: O)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADZ4 Pfam ID:PF00312

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:U (auth: P)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7T3 Pfam ID:PF00886

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsQ
Chain IDs:V (auth: Q)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG63 Pfam ID:PF00366

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsR
Chain IDs:W (auth: R)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7T7 Pfam ID:PF01084

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsS
Chain IDs:X (auth: S)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7U3 Pfam ID:PF00203

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:Y (auth: T)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7U7 Pfam ID:PF01649

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Small ribosomal subunit prote
Gene (Uniprot):rpsU
Chain IDs:BB (auth: U)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P68679 Pfam ID:PF01165

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:Z (auth: X)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:fMet-Initiator P-site tRNA
Chain IDs:AA (auth: Z)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:F (auth: a)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Polymer Type:polyribonucleotide
Molecule:5s rRNA
Chain IDs:BA (auth: b)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplB
Chain IDs:CA (auth: c)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplC
Chain IDs:C (auth: d)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60438 Pfam ID:PF00297

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplD
Chain IDs:DA (auth: e)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60723 Pfam ID:PF00573

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplE
Chain IDs:EA (auth: f)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplF
Chain IDs:FA (auth: g)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG55 Pfam ID:PF00347

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplI
Chain IDs:GA (auth: h)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplM
Chain IDs:HA (auth: i)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AA10 Pfam ID:PF00572

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplN
Chain IDs:IA (auth: j)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADY3 Pfam ID:PF00238

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:JA (auth: k)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P02413 Pfam ID:PF00828

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplP
Chain IDs:YA (auth: l)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADY7 Pfam ID:PF00252

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplQ
Chain IDs:KA (auth: m)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG44 Pfam ID:PF01196

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplR
Chain IDs:LA (auth: n)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0C018 Pfam ID:PF00861

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplS
Chain IDs:MA (auth: o)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7K6 Pfam ID:PF01245

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplT
Chain IDs:NA (auth: p)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7L3 Pfam ID:PF00453

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplU
Chain IDs:OA (auth: q)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG48 Pfam ID:PF00829

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplV
Chain IDs:PA (auth: r)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P61175 Pfam ID:PF00237

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplW
Chain IDs:QA (auth: s)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0ADZ0 Pfam ID:PF00276

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rplX
Chain IDs:RA (auth: t)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:SA (auth: u)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P68919 Pfam ID:PF01386

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmA
Chain IDs:TA (auth: v)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7L8 Pfam ID:PF01016

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmB
Chain IDs:UA (auth: w)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7M2 Pfam ID:PF00830

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmC
Chain IDs:VA (auth: x)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0A7M6 Pfam ID:PF00831

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmD
Chain IDs:WA (auth: y)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113

UniProt ID:P0AG51 Pfam ID:PF00327

Structures with similar UniProt ID

Structural Superimposition Protein Blast

Polymer Type:polypeptide(L)
Molecule:Large ribosomal subunit prote
Gene (Uniprot):rpmF
Chain IDs:XA (auth: z)
Chain Length:0
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
4D4	YA	ARG	modified residue
D2T	B	ASP	modified residue
MEQ	C	GLN	modified residue

Ligand Molecules

Primary Citation

Flipping antimicrobial peptides in the exit tunnel of the bacterial ribosome.

Huang, W, Berger, M.J, Safdari, H.A, Klepacki, D, Paternoga, H, Baliga, C, Wilson, D.N, Vazquez-Laslop, N, Mankin, A.S.Show

Nat Commun 17 ? ? (2026)

PMID: 42236475 DOI: 10.1038/s41467-026-74007-x

Abstact

Proline-rich antimicrobial peptides (PrAMPs) kill bacteria by binding in the ribosomal nascent peptide exit tunnel. Type II PrAMPs bind in an orientation matching that of the nascent protein, trap the release factors and arrest ribosomes at stop codons. Conversely, Type I PrAMPs bind in an opposite orientation: their N-terminus invades the peptidyl transferase center arresting translation at start codons. Here, by mining the genome databases, we identify a number of PrAMPs with high sequence similarity to the Type II PrAMP Drosocin. Notably, many of the new PrAMPs do not stall ribosomes at stop codons, but act as Type I PrAMPs arresting translation at start codons. Structural analysis shows that such peptides bind with a Type I orientation. Minimal alterations in the peptide structure can flip the orientation of the PrAMP in the exit tunnel, switching the mechanism of translation inhibition. Altering the mode of binding and action of a PrAMP by only few mutations could be exploited by the host to combat newly emerging bacterial pathogens.

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Protein

Chemical

Disease

Primary Citation of related structures

Abstact

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