6HA1

Cryo-EM structure of a 70S Bacillus subtilis ribosome translating the ErmD leader peptide in complex with telithromycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for antibiotic resistance mediated by theBacillus subtilisABCF ATPase VmlR.

Crowe-McAuliffe, C.Graf, M.Huter, P.Takada, H.Abdelshahid, M.Novacek, J.Murina, V.Atkinson, G.C.Hauryliuk, V.Wilson, D.N.

(2018) Proc Natl Acad Sci U S A 115: 8978-8983

  • DOI: 10.1073/pnas.1808535115
  • Primary Citation of Related Structures:  
    6HA8, 6HA1

  • PubMed Abstract: 
  • Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In Bacillus subtilis , the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S ...

    Many Gram-positive pathogenic bacteria employ ribosomal protection proteins (RPPs) to confer resistance to clinically important antibiotics. In Bacillus subtilis , the RPP VmlR confers resistance to lincomycin (Lnc) and the streptogramin A (S A ) antibiotic virginiamycin M (VgM). VmlR is an ATP-binding cassette (ABC) protein of the F type, which, like other antibiotic resistance (ARE) ABCF proteins, is thought to bind to antibiotic-stalled ribosomes and promote dissociation of the drug from its binding site. To investigate the molecular mechanism by which VmlR confers antibiotic resistance, we have determined a cryo-electron microscopy (cryo-EM) structure of an ATPase-deficient B. subtilis VmlR-EQ 2 mutant in complex with a B. subtilis ErmDL-stalled ribosomal complex (SRC). The structure reveals that VmlR binds within the E site of the ribosome, with the antibiotic resistance domain (ARD) reaching into the peptidyltransferase center (PTC) of the ribosome and a C-terminal extension (CTE) making contact with the small subunit (SSU). To access the PTC, VmlR induces a conformational change in the P-site tRNA, shifting the acceptor arm out of the PTC and relocating the CCA end of the P-site tRNA toward the A site. Together with microbiological analyses, our study indicates that VmlR allosterically dissociates the drug from its ribosomal binding site and exhibits specificity to dislodge VgM, Lnc, and the pleuromutilin tiamulin (Tia), but not chloramphenicol (Cam), linezolid (Lnz), nor the macrolide erythromycin (Ery).


    Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, 20146 Hamburg, Germany; daniel.wilson@chemie.uni-hamburg.de.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C277Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplBBSU01190
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Entity ID: 4
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50S ribosomal protein L3D209Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplCBSU01160
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Entity ID: 5
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50S ribosomal protein L4E207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplDBSU01170
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplEBSU01280
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Entity ID: 7
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50S ribosomal protein L6G179Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplFBSU01310
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Entity ID: 8
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50S ribosomal protein L13J145Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplMBSU01490
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Entity ID: 9
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50S ribosomal protein L14K122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplNBSU01260
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Entity ID: 10
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50S ribosomal protein L15L146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplOBSU01350
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Entity ID: 11
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50S ribosomal protein L16M144Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplPBSU01230
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Entity ID: 12
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50S ribosomal protein L17N120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplQBSU01440
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Entity ID: 13
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50S ribosomal protein L18O120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplRBSU01320
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Entity ID: 14
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50S ribosomal protein L19P115Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplSBSU16040
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Entity ID: 15
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50S ribosomal protein L20Q119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplTBSU28850
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Entity ID: 16
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50S ribosomal protein L21R102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplUBSU27960
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Entity ID: 17
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50S ribosomal protein L22S113Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplVBSU01210
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Entity ID: 18
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50S ribosomal protein L23T95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplWBSU01180
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Entity ID: 19
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50S ribosomal protein L24U103Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplXBSU01270
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Entity ID: 20
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50S ribosomal protein L27W94Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmABSU27940
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Entity ID: 21
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50S ribosomal protein L28X62Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmByloTBSU15820
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Entity ID: 22
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50S ribosomal protein L29Y66Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmCBSU01240
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Entity ID: 23
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50S ribosomal protein L30Z59Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmDBSU01340
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Entity ID: 24
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50S ribosomal protein L32059Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmFBSU15080
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Entity ID: 25
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50S ribosomal protein L33 1149Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmGArpmG1BSU24900
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Entity ID: 26
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50S ribosomal protein L34244Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmHBSU41060
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Entity ID: 27
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50S ribosomal protein L35366Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmIBSU28860
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Entity ID: 28
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50S ribosomal protein L36437Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmJBSU01400
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Entity ID: 29
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50S ribosomal protein L31663Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmEBSU37070
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Entity ID: 32
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30S ribosomal protein S2b246Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsBBSU16490
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Entity ID: 33
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30S ribosomal protein S3c218Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsCBSU01220
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Entity ID: 34
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30S ribosomal protein S4d200Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsDBSU29660
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Entity ID: 35
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30S ribosomal protein S5e166Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsEspcABSU01330
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Entity ID: 36
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30S ribosomal protein S6f95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsFBSU40910
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Entity ID: 37
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30S ribosomal protein S7g156Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsGBSU01110
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Entity ID: 38
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30S ribosomal protein S8h132Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsHBSU01300
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Entity ID: 39
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30S ribosomal protein S9i130Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsIBSU01500
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Entity ID: 40
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30S ribosomal protein S10j102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsJtetABSU01150
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Entity ID: 41
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30S ribosomal protein S11k131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsKBSU01420
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Entity ID: 42
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30S ribosomal protein S12l138Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsLfunstrABSU01100
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Entity ID: 43
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30S ribosomal protein S13m121Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsMBSU01410
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Entity ID: 44
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30S ribosomal protein S14n61Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsN1rpsNrpsNArpsZBSU01290
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Entity ID: 45
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30S ribosomal protein S15o89Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsOBSU16680
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Entity ID: 46
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30S ribosomal protein S16p90Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsPBSU15990
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Entity ID: 47
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30S ribosomal protein S17q87Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsQBSU01250
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Entity ID: 48
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30S ribosomal protein S18r79Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsRBSU40890
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Entity ID: 49
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30S ribosomal protein S19s92Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsSBSU01200
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Entity ID: 50
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30S ribosomal protein S20t88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsTyqeOBSU25550
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Entity ID: 1
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23S ribosomal RNAA2928Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 2
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5S ribosomal RNAB112Bacillus subtilis subsp. subtilis str. 168
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  • Entity ID: 30
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    mRNA73Bacillus subtilis subsp. subtilis str. 168
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    Entity ID: 31
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    16S ribosomal RNAa1554Bacillus subtilis subsp. subtilis str. 168
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    Entity ID: 51
    MoleculeChainsLengthOrganismImage
    P-tRNAx87Escherichia coli
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TEL
    Query on TEL

    Download CCD File 
    A
    TELITHROMYCIN
    C43 H65 N5 O10
    LJVAJPDWBABPEJ-MMEUOAQYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.10 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

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    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    German Research FoundationGermanyFOR1805
    German Research FoundationGermanyWI3285/6-1
    Ministry of Education (Czech Republic)Czech RepublicCIISB project number LM2015043
    European UnionCzech RepubliciNext project number 2992

    Revision History 

    • Version 1.0: 2018-08-29
      Type: Initial release
    • Version 1.1: 2018-09-12
      Changes: Data collection, Database references
    • Version 1.2: 2019-12-11
      Changes: Other