1XMQ

Crystal Structure of t6A37-ASLLysUUU AAA-mRNA Bound to the Decoding Center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.222 

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This is version 1.2 of the entry. See complete history


Literature

The role of modifications in codon discrimination by tRNA(Lys)(UUU).

Murphy, F.V.Ramakrishnan, V.Malkiewicz, A.Agris, P.F.

(2004) Nat Struct Mol Biol 11: 1186-1191

  • DOI: 10.1038/nsmb861
  • Primary Citation of Related Structures:  
    1XMQ, 1XMO

  • PubMed Abstract: 
  • The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNA(Lys)(UUU) requires the modification N6-threonylcarbamoyladenosine at position 37 (t(6)A37), adjacent and 3' to the ...

    The natural modification of specific nucleosides in many tRNAs is essential during decoding of mRNA by the ribosome. For example, tRNA(Lys)(UUU) requires the modification N6-threonylcarbamoyladenosine at position 37 (t(6)A37), adjacent and 3' to the anticodon, to bind AAA in the A site of the ribosomal 30S subunit. Moreover, it can only bind both AAA and AAG lysine codons when doubly modified with t(6)A37 and either 5-methylaminomethyluridine or 2-thiouridine at the wobble position (mnm(5)U34 or s(2)U34). Here we report crystal structures of modified tRNA anticodon stem-loops bound to the 30S ribosomal subunit with lysine codons in the A site. These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG.


    Organizational Affiliation

    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S2B256Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S3C239Thermus thermophilusMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S4D209Thermus thermophilusMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S5E162Thermus thermophilusMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S6F101Thermus thermophilusMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S7G156Thermus thermophilusMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S8H138Thermus thermophilusMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S9I128Thermus thermophilusMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S10J105Thermus thermophilusMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S11K129Thermus thermophilusMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S12L135Thermus thermophilusMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S13M126Thermus thermophilusMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S14N61Thermus thermophilusMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S15O89Thermus thermophilusMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S16P88Thermus thermophilusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S17Q105Thermus thermophilusMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S18R88Thermus thermophilusMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S19S93Thermus thermophilusMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein S20T106Thermus thermophilusMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal Protein ThxV27Thermus thermophilusMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16s ribosomal RNAA1522Thermus thermophilus HB8
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    A-Site Messenger RNAW4N/A
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      Anticodon RNAX11N/A
      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, N, X
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.00 Å
      • R-Value Free: 0.236 
      • R-Value Work: 0.222 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 400.723α = 90
      b = 400.723β = 90
      c = 175.088γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNSrefinement
      CNSphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2004-12-14
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Source and taxonomy, Version format compliance