RCSB PDB - 9HA4: Pooled 50S subunit C-CP_(L22)- precursor states supplemented with Api137

 9HA4

Pooled 50S subunit C-CP_(L22)- precursor states supplemented with Api137


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The proline-rich antimicrobial peptide Api137 disrupts large ribosomal subunit assembly and induces misfolding.

Lauer, S.M.Gasse, J.Krizsan, A.Reepmeyer, M.Sprink, T.Nikolay, R.Spahn, C.M.T.Hoffmann, R.

(2025) Nat Commun 16: 567

  • DOI: https://doi.org/10.1038/s41467-025-55836-8
  • Primary Citation of Related Structures:  
    9H3K, 9H3L, 9H3M, 9H3N, 9H3O, 9H3P, 9H3Q, 9H3R, 9H3S, 9H3T, 9H3U, 9H3V, 9H3W, 9H3X, 9H3Y, 9H3Z, 9HA1, 9HA2, 9HA3, 9HA4, 9HA5, 9HA6, 9HA7, 9HAI, 9HAL, 9HAM

  • PubMed Abstract: 

    The proline-rich antimicrobial designer peptide Api137 inhibits protein expression in bacteria by binding simultaneously to the ribosomal polypeptide exit tunnel and the release factor (RF), depleting the cellular RF pool and leading to ribosomal arrest at stop codons. This study investigates the additional effect of Api137 on the assembly of ribosomes using an Escherichia coli reporter strain expressing one ribosomal protein per 30S and 50S subunit tagged with mCherry and EGFP, respectively. Separation of cellular extracts derived from cells exposed to Api137 in a sucrose gradient reveals elevated levels of partially assembled and not fully matured precursors of the 50S subunit (pre-50S). High-resolution structures obtained by cryogenic electron microscopy demonstrate that a large proportion of pre-50S states are missing up to five proteins (uL22, bL32, uL29, bL23, and uL16) and have misfolded helices in 23S rRNA domain IV. These data suggest a second mechanism for Api137, wherein it disrupts 50S subunit assembly by inducing the formation of misfolded precursor particles potentially incapable of evolving into active ribosomes, suggesting a bactericidal mechanism.


  • Organizational Affiliation

    Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34A [auth 2]46Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3C [auth D]209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5D [auth F]177Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13E [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14F [auth K]122Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17G [auth N]120Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18H [auth O]116Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19I [auth P]114Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20J [auth Q]117Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21K [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23L [auth T]93Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24M [auth U]102Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25N [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27O [auth W]75Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29P [auth Y]63Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30Q [auth Z]58Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Apidaecins type 22R [auth y]17Apis melliferaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4T [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15U [auth L]143Escherichia coliMutation(s): 0 
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.26 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany16GW0300
German Federal Ministry for Education and ResearchGermany16GW0299K
German Research Foundation (DFG)GermanyEXC2008/1-390540038
German Research Foundation (DFG)GermanyINST 335/588-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release