5KCR

Cryo-EM structure of the Escherichia coli 70S ribosome in complex with antibiotic Avilamycin C, mRNA and P-site tRNA at 3.6A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome.

Arenz, S.Juette, M.F.Graf, M.Nguyen, F.Huter, P.Polikanov, Y.S.Blanchard, S.C.Wilson, D.N.

(2016) Proc Natl Acad Sci U S A 113: 7527-7532

  • DOI: 10.1073/pnas.1604790113
  • Primary Citation of Related Structures:  
    5KCR, 5KCS

  • PubMed Abstract: 
  • The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ...

    The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis.


    Organizational Affiliation

    Gene Center and Department for Biochemistry, University of Munich, 81377 Munich, Germany; Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany wilson@lmb.uni-muenchen.de yuryp@uic.edu scb2005@med.cornell.edu.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21D273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 4
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50S ribosomal protein L31E209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 5
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50S ribosomal protein L41F201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 6
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50S ribosomal protein L51G179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 7
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50S ribosomal protein L61H177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 8
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50S ribosomal protein L91I149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 9
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50S ribosomal protein L101J165Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
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Entity ID: 10
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50S ribosomal protein L111K142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 11
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50S ribosomal protein L131N142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 12
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50S ribosomal protein L141O123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 13
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50S ribosomal protein L151P144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 14
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50S ribosomal protein L161Q136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 15
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50S ribosomal protein L171R127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 16
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50S ribosomal protein L181S117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L191T115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 18
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50S ribosomal protein L201U118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 19
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50S ribosomal protein L211V103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L221W110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L231X100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L241Y104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L251Z94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L271085Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 25
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50S ribosomal protein L281178Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 26
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50S ribosomal protein L291263Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L301359Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L321557Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L331655Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 30
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50S ribosomal protein L341746Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L351865Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L361938Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 34
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30S ribosomal protein S21b241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 35
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30S ribosomal protein S31c233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 36
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30S ribosomal protein S41d206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 37
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30S ribosomal protein S51e167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 38
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30S ribosomal protein S61f135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S71g179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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30S ribosomal protein S81h130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S91i130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 42
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30S ribosomal protein S101j103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 43
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30S ribosomal protein S111k129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 44
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30S ribosomal protein S121l124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 45
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30S ribosomal protein S131m118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 46
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30S ribosomal protein S141n101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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30S ribosomal protein S151o89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 48
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30S ribosomal protein S161p82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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30S ribosomal protein S171q84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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30S ribosomal protein S181r75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 51
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30S ribosomal protein S191s92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 52
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30S ribosomal protein S201t87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 53
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30S ribosomal protein S211u71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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23S Ribosomal RNA1A2904Escherichia coli K-12
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5S Ribosomal RNA1B120Escherichia coli K-12
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16S Ribosomal RNA1a1539Escherichia coli K-12
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    mRNA1v9synthetic construct
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    Entity ID: 55
    MoleculeChainsLengthOrganismImage
    P-site tRNA1x87Escherichia coli K-12
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    6UQ
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    1A
    (2R,3S,4R,6S)-4-hydroxy-6-{[(2R,3aR,4R,4'R,5'S,6S,6'R,7aR)-4'-hydroxy-6-{[(2S,3R,4R,5S,6R)-3-hydroxy-2-{[(2R,3S,4S,5S,6S)-4-hydroxy-6-({(2R,3aS,3a'R,6S,6'R,7R,7'R,7aR,7a'R)-7'-hydroxy-7'-[(1S)-1-hydroxyethyl]-6'-methyl-7-[(2-methylpropanoyl)oxy]octahydro-4H-2,4'-spirobi[[1,3]dioxolo[4,5-c]pyran]-6-yl}oxy)-5-methoxy-2-(methoxymethyl)tetrahydro-2H-pyran-3-yl]oxy}-5-methoxy-6-methyltetrahydro-2H-pyran-4-yl]oxy}-4,6',7a-trimethyloctahydro-4H-spiro[1,3-dioxolo[4,5-c]pyran-2,2'-pyran]-5'-yl]oxy}-2-methyltetrahydro-2H-pyran-3-yl 3,5-dichloro-4-hydroxy-2-methoxy-6-methylbenzoate (non-preferred name)
    C61 H90 Cl2 O32
    AEIFATUAVHHRBC-JOYRSTEWSA-N
     Ligand Interaction
    ZN
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    19
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    MEQ
    Query on MEQ
    1EL-PEPTIDE LINKINGC6 H12 N2 O3GLN
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.60 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Illinois State Startup FundsUnited States--
    German Research Foundation (DFG)GermanyFOR1805
    German Research Foundation (DFG)GermanyWI3285/3-2
    German Research Foundation (DFG)GermanyGRK1721
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM079238
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098859

    Revision History 

    • Version 1.0: 2016-08-17
      Type: Initial release
    • Version 1.1: 2017-09-27
      Changes: Author supporting evidence, Data collection
    • Version 2.0: 2018-05-16
      Changes: Data collection, Polymer sequence, Source and taxonomy
    • Version 2.1: 2018-07-18
      Changes: Data collection
    • Version 2.2: 2019-12-25
      Changes: Author supporting evidence