RCSB PDB - 9H3S: 50S subunit precursor C-CP_YjgA_L22

 9H3S

50S subunit precursor C-CP_YjgA_L22

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-10-17 Released: 2025-01-22 
  • Deposition Author(s): Lauer, S., Nikolay, R., Spahn, C.M.T.
  • Funding Organization(s): German Federal Ministry for Education and Research, German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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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: 567-567

  • 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 bL32A [auth 0]56Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL34B [auth 2]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL36AC [auth 4]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0307 protein YjgAF [auth C]183Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A8X0 (Escherichia coli (strain K12))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3G [auth D]209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4H [auth E]201Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5I [auth F]177Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6J [auth G]176Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9K [auth H]149Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13L [auth J]142Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14M [auth K]122Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15N [auth L]143Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17O [auth N]120Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18P [auth O]116Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL19Q [auth P]114Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20R [auth Q]117Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21S [auth R]103Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22T [auth S]110Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23U [auth T]93Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24V [auth U]102Escherichia coliMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25W [auth V]94Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27X [auth W]75Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL28Y [auth X]77Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29Z [auth Y]63Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30AA [auth Z]58Escherichia coliMutation(s): 0 
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21-5207

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: 2025-01-22
    Type: Initial release