1FJG

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH THE ANTIBIOTICS STREPTOMYCIN, SPECTINOMYCIN, AND PAROMOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics

Carter, A.P.Clemons Jr., W.M.Brodersen, D.E.Morgan-Warren, R.J.Wimberly, B.T.Ramakrishnan, V.

(2000) Nature 407: 340-348

  • DOI: 10.1038/35030019
  • Primary Citation of Related Structures:  
    1FJG

  • PubMed Abstract: 
  • The 30S ribosomal subunit has two primary functions in protein synthesis. It discriminates against aminoacyl transfer RNAs that do not match the codon of messenger RNA, thereby ensuring accuracy in translation of the genetic message in a process called decoding ...

    The 30S ribosomal subunit has two primary functions in protein synthesis. It discriminates against aminoacyl transfer RNAs that do not match the codon of messenger RNA, thereby ensuring accuracy in translation of the genetic message in a process called decoding. Also, it works with the 50S subunit to move the tRNAs and associated mRNA by precisely one codon, in a process called translocation. Here we describe the functional implications of the high-resolution 30S crystal structure presented in the accompanying paper, and infer details of the interactions between the 30S subunit and its tRNA and mRNA ligands. We also describe the crystal structure of the 30S subunit complexed with the antibiotics paromomycin, streptomycin and spectinomycin, which interfere with decoding and translocation. This work reveals the structural basis for the action of these antibiotics, and leads to a model for the role of the universally conserved 16S RNA residues A1492 and A1493 in the decoding process.


    Related Citations: 
    • Structure of the 30S Ribosomal Subunit
      Wimberly, B.T., Brodersen, D.E., Clemons Jr., W.M., Morgan-Warren, R., Carter, A.P., Vonrhein, C., Hartsch, T., Ramakrishnan, V.
      (2000) Nature 407: 327
    • Structure of a Bacterial 30S Ribosomal Subunit at 5.5A Resolution
      Clemons Jr., W.M., May, J.L.C., Wimberly, B.T., McCutcheon, J.P., Capel, M.S., Ramakrishnan, V.
      (1999) Nature 400: 833

    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2C [auth B]256Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3D [auth C]239Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4E [auth D]209Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5F [auth E]162Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6G [auth F]101Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7H [auth G]156Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8I [auth H]138Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9J [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10K [auth J]105Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11L [auth K]129Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12M [auth L]135Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13N [auth M]126Thermus thermophilusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14O [auth N]61Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15P [auth O]89Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16Q [auth P]88Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17R [auth Q]105Thermus thermophilusMutation(s): 0 
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Entity ID: 19
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30S RIBOSOMAL PROTEIN S18S [auth R]88Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19T [auth S]93Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20U [auth T]106Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXV26Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1522Thermus thermophilus
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    FRAGMENT OF MESSENGER RNAB [auth X]6Thermus thermophilus
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 5 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PAR
    Query on PAR

    Download Ideal Coordinates CCD File 
    W [auth A]PAROMOMYCIN
    C23 H45 N5 O14
    UOZODPSAJZTQNH-LSWIJEOBSA-N
     Ligand Interaction
    SRY
    Query on SRY

    Download Ideal Coordinates CCD File 
    OD [auth A]STREPTOMYCIN
    C21 H39 N7 O12
    UCSJYZPVAKXKNQ-HZYVHMACSA-N
     Ligand Interaction
    SCM
    Query on SCM

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    ND [auth A]SPECTINOMYCIN
    C14 H24 N2 O7
    UNFWWIHTNXNPBV-WXKVUWSESA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    QD [auth D], SD [auth N]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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    AA [auth A] , AB [auth A] , AC [auth A] , AD [auth A] , BA [auth A] , BB [auth A] , BC [auth A] , BD [auth A] , 
    AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  HA [auth A],  HB [auth A],  HC [auth A],  HD [auth A],  IA [auth A],  IB [auth A],  IC [auth A],  ID [auth A],  JA [auth A],  JB [auth A],  JC [auth A],  JD [auth A],  KA [auth A],  KB [auth A],  KC [auth A],  KD [auth A],  LA [auth A],  LB [auth A],  LC [auth A],  LD [auth A],  MA [auth A],  MB [auth A],  MC [auth A],  MD [auth A],  NA [auth A],  NB [auth A],  NC [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth D],  QA [auth A],  QB [auth A],  QC [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth H],  SA [auth A],  SB [auth A],  SC [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  VA [auth A],  VB [auth A],  VC [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  X [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Free: 0.255 
    • R-Value Work: 0.221 
    • R-Value Observed: 0.221 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 402.001α = 90
    b = 402.001β = 90
    c = 176.489γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    SCALEPACKdata scaling
    CNSrefinement
    HKL-2000data reduction
    CNSphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-09-25
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance