5O2R

Cryo-EM structure of the proline-rich antimicrobial peptide Api137 bound to the terminating ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome.

Florin, T.Maracci, C.Graf, M.Karki, P.Klepacki, D.Berninghausen, O.Beckmann, R.Vazquez-Laslop, N.Wilson, D.N.Rodnina, M.V.Mankin, A.S.

(2017) Nat Struct Mol Biol 24: 752-757

  • DOI: https://doi.org/10.1038/nsmb.3439
  • Primary Citation of Related Structures:  
    5O2R

  • PubMed Abstract: 
  • Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of multicellular organisms, interfere with bacterial growth by inhibiting translation ...

    Many antibiotics stop bacterial growth by inhibiting different steps of protein synthesis. However, no specific inhibitors of translation termination are known. Proline-rich antimicrobial peptides, a component of the antibacterial defense system of multicellular organisms, interfere with bacterial growth by inhibiting translation. Here we show that Api137, a derivative of the insect-produced antimicrobial peptide apidaecin, arrests terminating ribosomes using a unique mechanism of action. Api137 binds to the Escherichia coli ribosome and traps release factor (RF) RF1 or RF2 subsequent to the release of the nascent polypeptide chain. A high-resolution cryo-EM structure of the ribosome complexed with RF1 and Api137 reveals the molecular interactions that lead to RF trapping. Api137-mediated depletion of the cellular pool of free release factors causes the majority of ribosomes to stall at stop codons before polypeptide release, thereby resulting in a global shutdown of translation termination.


    Organizational Affiliation

    Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.



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50S ribosomal protein L2C271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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50S ribosomal protein L3D209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L4E201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L5F177Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6G176Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L16M136Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L17N120Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18O116Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L21R103Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L22S110Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L23T93Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L24U102Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L25V94Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L27W75Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L28X77Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L29Y63Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L30Z58Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L32AA [auth 0]56Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L33BA [auth 1]50Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L34CA [auth 2]46Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L35DA [auth 3]64Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L36EA [auth 4]38Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L10FA [auth 5]131Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L31GA [auth 6]66Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S2JA [auth b]218Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S3KA [auth c]206Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S4LA [auth d]205Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S5MA [auth e]157Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S6NA [auth f]100Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S7OA [auth g]151Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8PA [auth h]129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S9QA [auth i]127Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S10RA [auth j]98Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11SA [auth k]116Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S12TA [auth l]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13UA [auth m]114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 48
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30S ribosomal protein S14VA [auth n]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 49
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30S ribosomal protein S15WA [auth o]88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 50
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30S ribosomal protein S16XA [auth p]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 51
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30S ribosomal protein S17YA [auth q]80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18ZA [auth r]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 53
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30S ribosomal protein S19AB [auth s]79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 54
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30S ribosomal protein S20BB [auth t]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 55
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30S ribosomal protein S21CB [auth u]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 56
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Peptide chain release factor RF1DB [auth v]242Escherichia coli K-12Mutation(s): 0 
Gene Names: prfAsueBuarb1211JW1202
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
ApidaecinFB [auth z]14Apis melliferaMutation(s): 0 
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Entity ID: 1
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23S ribosomal RNAA2,903Escherichia coli K-12
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Entity ID: 2
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5S ribosomal RNAB120Escherichia coli K-12
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Entity ID: 34
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mRNAHA [auth 7]7Staphylococcus aureus
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Entity ID: 35
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16S ribosomal RNAIA [auth a]1,539Escherichia coli K-12
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Entity ID: 57
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P-site Ile-tRNAEB [auth x]77Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONFREALIGN9.11
MODEL REFINEMENTPHENIX1.11.1-2575

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
iNEXTCzech RepublicProject 2259
German Research FoundationGermanyFOR1805

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations