1IBK

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH THE ANTIBIOTIC PAROMOMYCIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of cognate transfer RNA by the 30S ribosomal subunit.

Ogle, J.M.Brodersen, D.E.Clemons Jr., W.M.Tarry, M.J.Carter, A.P.Ramakrishnan, V.

(2001) Science 292: 897-902

  • DOI: 10.1126/science.1060612
  • Primary Citation of Related Structures:  
    1IBM, 1IBL, 1IBK

  • PubMed Abstract: 
  • Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA ...

    Crystal structures of the 30S ribosomal subunit in complex with messenger RNA and cognate transfer RNA in the A site, both in the presence and absence of the antibiotic paromomycin, have been solved at between 3.1 and 3.3 angstroms resolution. Cognate transfer RNA (tRNA) binding induces global domain movements of the 30S subunit and changes in the conformation of the universally conserved and essential bases A1492, A1493, and G530 of 16S RNA. These bases interact intimately with the minor groove of the first two base pairs between the codon and anticodon, thus sensing Watson-Crick base-pairing geometry and discriminating against near-cognate tRNA. The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs.


    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
    • 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., Wimberly, B.T., Morgan-Warren, R., Ramakrishnan, V.
      (2000) Nature 407: 340

    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2C [auth B]256Thermus thermophilusMutation(s): 0 
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3D [auth C]239Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4E [auth D]209Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5F [auth E]162Thermus thermophilusMutation(s): 0 
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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 
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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 
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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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 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15P [auth O]89Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16Q [auth P]88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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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
MoleculeChainsSequence LengthOrganismDetailsImage
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 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20U [auth T]106Thermus thermophilusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXV26Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1522Thermus thermophilus
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    P-SITE MESSENGER RNA FRAGMENTB [auth X]6Thermus thermophilus
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 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
    ZN
    Query on ZN

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

    Download Ideal Coordinates CCD File 
    AA [auth A] , AB [auth A] , AC [auth A] , AD [auth A] , AE [auth A] , BA [auth A] , BB [auth A] , BC [auth A] , 
    AA [auth A],  AB [auth A],  AC [auth A],  AD [auth A],  AE [auth A],  BA [auth A],  BB [auth A],  BC [auth A],  BD [auth A],  BE [auth A],  CA [auth A],  CB [auth A],  CC [auth A],  CD [auth A],  CE [auth A],  DA [auth A],  DB [auth A],  DC [auth A],  DD [auth A],  DE [auth A],  EA [auth A],  EB [auth A],  EC [auth A],  ED [auth A],  EE [auth D],  FA [auth A],  FB [auth A],  FC [auth A],  FD [auth A],  GA [auth A],  GB [auth A],  GC [auth A],  GD [auth A],  GE [auth L],  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],  ND [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth A],  PA [auth A],  PB [auth A],  PC [auth A],  PD [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth A],  RA [auth A],  RB [auth A],  RC [auth A],  RD [auth A],  SA [auth A],  SB [auth A],  SC [auth A],  SD [auth A],  TA [auth A],  TB [auth A],  TC [auth A],  TD [auth A],  UA [auth A],  UB [auth A],  UC [auth A],  UD [auth A],  VA [auth A],  VB [auth A],  VC [auth A],  VD [auth A],  WA [auth A],  WB [auth A],  WC [auth A],  WD [auth A],  X [auth A],  XA [auth A],  XB [auth A],  XC [auth A],  XD [auth A],  Y [auth A],  YA [auth A],  YB [auth A],  YC [auth A],  YD [auth A],  Z [auth A],  ZA [auth A],  ZB [auth A],  ZC [auth A],  ZD [auth A]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.31 Å
    • R-Value Free: 0.282 
    • R-Value Work: 0.229 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 401.16α = 90
    b = 401.16β = 90
    c = 176.36γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data collection
    SCALEPACKdata scaling
    CNSrefinement
    HKL-2000data reduction
    CNSphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2001-05-04
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance