9TEY image
Deposition Date 2025-11-26
Release Date 2026-07-22
Last Version Date 2026-07-22
Entry Detail
PDB ID:
9TEY
Keywords:
ANTIBIOTIC
Title:
DalDro bound to the terminating Escherichia coli 70S ribosome
Biological Source:
Source Organism(s):
Escherichia coli BW25113 (Taxon ID: 679895)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.11 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9TEY validation report missing
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:A (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:B (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:C (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:D (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:AB (auth: 4)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7M9 Pfam ID:PF01197
Structures with similar UniProt ID
Structural Superimposition Protein Blast
Polymer Type:polypeptide(L)
Molecule:Drosocin
Gene (Uniprot):Dro
Chain IDs:E (auth: 8)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P36193
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:CB (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:F (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:G (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:H (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:I (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:J (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:K (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:L (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:M (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:N (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:O (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:P (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:Q (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:R (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:S (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:T (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:U (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:V (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:W (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:X (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:Y (auth: U)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P68679 Pfam ID:PF01165
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:BB (auth: V)
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:Peptide chain release factor
Gene (Uniprot):prfA
Chain IDs:Z (auth: W)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113
UniProt ID:P0A7I0 Pfam ID:PF03462, PF00472
Polymer Type:polyribonucleotide
Molecule:P-site Phe-tRNA
Chain IDs:AA (auth: Z)
Chain Length:0
Number of Molecules:1
Biological Source:Escherichia coli BW25113
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:BA (auth: b), DB (auth: Y)
Chain Length:0
Number of Molecules:2
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:DA (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:EA (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:FA (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:GA (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:HA (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:IA (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:JA (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:KA (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:LA (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:MA (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:NA (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:OA (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:PA (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:QA (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:RA (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:SA (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:TA (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:UA (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:VA (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:WA (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:XA (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:YA (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:ZA (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 2D Image
4D4 LA ARG modified residue
D2T P ASP modified residue
MEQ DA GLN modified residue
MS6 LA MET modified residue
Ligand Molecules
SPM
ZN
Primary Citation
Flipping antimicrobial peptides in the exit tunnel of the bacterial ribosome.
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
9TEY
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