1HNW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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This is version 1.2 of the entry. See complete history


Literature

The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit.

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

(2000) Cell 103: 1143-1154

  • DOI: 10.1016/s0092-8674(00)00216-6
  • Primary Citation of Related Structures:  
    1HNZ, 1HNX, 1HNW

  • PubMed Abstract: 
  • We have used the recently determined atomic structure of the 30S ribosomal subunit to determine the structures of its complexes with the antibiotics tetracycline, pactamycin, and hygromycin B. The antibiotics bind to discrete sites on the 30S subunit in a manner consistent with much but not all biochemical data ...

    We have used the recently determined atomic structure of the 30S ribosomal subunit to determine the structures of its complexes with the antibiotics tetracycline, pactamycin, and hygromycin B. The antibiotics bind to discrete sites on the 30S subunit in a manner consistent with much but not all biochemical data. For each of these antibiotics, interactions with the 30S subunit suggest a mechanism for its effects on ribosome function.


    Related Citations: 
    • The 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
    • 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, Hills Road, Cambridge CB2 2QH, United Kingdom.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2C [auth B]256Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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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 
UniProt
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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 
UniProt
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S9J [auth I]128Thermus thermophilusMutation(s): 0 
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S10K [auth J]105Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S11L [auth K]129Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12M [auth L]135Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S13N [auth M]126Thermus thermophilusMutation(s): 0 
UniProt
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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 
UniProt
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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 
UniProt
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Entity ID: 19
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30S RIBOSOMAL PROTEIN S18S [auth R]88Thermus thermophilusMutation(s): 0 
UniProt
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Entity ID: 20
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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
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    TAC (Subject of Investigation/LOI)
    Query on TAC

    Download Ideal Coordinates CCD File 
    MD [auth A], ND [auth A]TETRACYCLINE
    C22 H24 N2 O8
    OFVLGDICTFRJMM-WESIUVDSSA-N
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    PD [auth D], RD [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] , 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],  NA [auth A],  NB [auth A],  NC [auth A],  OA [auth A],  OB [auth A],  OC [auth A],  OD [auth D],  PA [auth A],  PB [auth A],  PC [auth A],  QA [auth A],  QB [auth A],  QC [auth A],  QD [auth H],  RA [auth A],  RB [auth A],  RC [auth A],  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],  W [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: 3.40 Å
    • R-Value Free: 0.264 
    • R-Value Work: 0.222 
    • R-Value Observed: 0.222 
    • Space Group: P 41 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 401.158α = 90
    b = 401.158β = 90
    c = 176.944γ = 90
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    CNSrefinement
    CNSphasing

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2001-02-21
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance