4WOI

4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions.

Wasserman, M.R.Pulk, A.Zhou, Z.Altman, R.B.Zinder, J.C.Green, K.D.Garneau-Tsodikova, S.Doudna Cate, J.H.Blanchard, S.C.

(2015) Nat Commun 6: 7896-7896

  • DOI: 10.1038/ncomms8896
  • Primary Citation of Related Structures:  
    4WOI

  • PubMed Abstract: 
  • Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we s ...

    Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.


    Organizational Affiliation

    1] Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA [2] Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.



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30S ribosomal protein S2ABDB241Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S3ACDC233Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S4ADDD206Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S5AEDE167Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S7AGDG179Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S20ATDT87Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S21AUDU71Escherichia coli K-12Mutation(s): 0 
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Ribosome-recycling factorAV185Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L2BCCC273Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L3BDCD209Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L4BECE201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L5BFCF179Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6BGCG177Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L9BHCH149Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L11BICI142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L13BJCJ142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14BKCK123Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L15BLCL144Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L16BMCM136Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L17BNCN127Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18BOCO117Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L19BPCP115Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L20BQCQ118Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L21BRCR103Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L22BSCS110Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L23BTCT100Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L24BUCU104Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L25BVCV94Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L27BWCW85Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L28BXCX78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29BYCY63Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L30BZCZ59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32B0C057Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33B1C155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34B2C246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35B3C365Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36B4C438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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50S ribosomal protein L1B5228Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SLP7 
Go to UniProtKB:  Q5SLP7
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAAA, DA1542Escherichia coli str. K-12 substr. MDS42
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  • Entity ID: 23
    MoleculeChainsLengthOrganismImage
    Messenger RNAAW, DV16Enterobacteria phage L1
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    Entity ID: 24
    MoleculeChainsLengthOrganismImage
    Phenylalanine specific transfer RNA, tRNA-PheAX, DW76Escherichia coli str. K-12 substr. MDS42
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    Entity ID: 25
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNABA, CA2904Escherichia coli str. K-12 substr. MDS42
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    Entity ID: 26
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNABB, CB120Escherichia coli str. K-12 substr. MDS42
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PAR
    Query on PAR

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    AA, BA, CA, DA
    PAROMOMYCIN
    C23 H45 N5 O14
    UOZODPSAJZTQNH-LSWIJEOBSA-N
     Ligand Interaction
    ZN
    Query on ZN

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    B4, C4
    ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    AA, AN, BA, BB, BL, BO, BQ, CA, CB, CD, CQ, DA, DD, DN
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Free: 0.253 
    • R-Value Work: 0.174 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 212.1α = 90
    b = 435.24β = 90
    c = 614.44γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XSCALEdata scaling
    PHENIXphasing
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2R01GM079238
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM65050
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States1R01AI090048
    National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA92584
    Human Frontiers in Science ProgramUnited StatesRGY0088
    National Science Foundation (NSF, United States)United States0644129
    Department of Energy (DOE, United States)United StatesDE-AC0376SF00098

    Revision History 

    • Version 1.0: 2015-08-05
      Type: Initial release
    • Version 1.1: 2015-08-12
      Changes: Database references
    • Version 1.2: 2017-09-20
      Changes: Author supporting evidence, Derived calculations, Refinement description
    • Version 1.3: 2019-11-27
      Changes: Author supporting evidence