1N33

Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form

Ogle, J.M.Murphy IV, F.V.Tarry, M.J.Ramakrishnan, V.

(2002) Cell 111: 721-732

  • DOI: 10.1016/s0092-8674(02)01086-3
  • Primary Citation of Related Structures:  
    1N34, 1N33, 1N32, 1N36

  • PubMed Abstract: 
  • A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center a ...

    A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.


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



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B256Thermus thermophilusMutation(s): 0 
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C239Thermus thermophilusMutation(s): 0 
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D208Thermus thermophilusMutation(s): 0 
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E161Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F101Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G155Thermus thermophilusMutation(s): 0 
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H138Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I128Thermus thermophilusMutation(s): 0 
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J104Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K129Thermus thermophilusMutation(s): 0 
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L135Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S13M126Thermus thermophilusMutation(s): 0 
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14N60Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q104Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R88Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S92Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20T106Thermus thermophilusMutation(s): 0 
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXV26Thermus thermophilusMutation(s): 0 
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RIBOSOMAL RNAA1522Thermus thermophilus
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    ANTICODON STEM-LOOP OF SER TRANSFER RNAY17Thermus thermophilus
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      A-SITE MESSENGER RNA FRAGMENTZ6Thermus thermophilus
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PAR
      Query on PAR

      Download CCD File 
      A
      PAROMOMYCIN
      C23 H45 N5 O14
      UOZODPSAJZTQNH-LSWIJEOBSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download CCD File 
      D, N
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      A, Y, Z
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      RNAKd :  86000   nM  PDBBind
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.35 Å
      • R-Value Free: 0.284 
      • R-Value Work: 0.225 
      • R-Value Observed: 0.225 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 401.599α = 90
      b = 401.599β = 90
      c = 176.025γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2002-11-29
        Type: Initial release
      • Version 1.1: 2008-04-28
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance