6MKN

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with an inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 2 (TRNAARG2) bound to an mRNA with an CGU-codon in the A-site and paromomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Structural Basis for Restricted Codon Recognition Mediated by 2-thiocytidine in tRNA Containing a Wobble Position Inosine.

Vangaveti, S.Cantara, W.A.Spears, J.L.DeMirci, H.Murphy IV, F.V.Ranganathan, S.V.Sarachan, K.L.Agris, P.F.

(2020) J Mol Biol 432: 913-929

  • DOI: 10.1016/j.jmb.2019.12.016
  • Primary Citation of Related Structures:  
    6MKN, 6MPI, 6MPF, 6DTI

  • PubMed Abstract: 
  • Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA Arg isoacceptors. The anticodon stem and loop (ASL) domains of tRNA Arg1 and tRNA Arg2 both contain inosine and 2-methyladen ...

    Three of six arginine codons (CGU, CGC, and CGA) are decoded by two Escherichia coli tRNA Arg isoacceptors. The anticodon stem and loop (ASL) domains of tRNA Arg1 and tRNA Arg2 both contain inosine and 2-methyladenosine modifications at positions 34 (I 34 ) and 37 (m 2 A 37 ). tRNA Arg1 is also modified from cytidine to 2-thiocytidine at position 32 (s 2 C 32 ). The s 2 C 32 modification is known to negate wobble codon recognition of the rare CGA codon by an unknown mechanism, while still allowing decoding of CGU and CGC. Substitution of s 2 C 32 for C 32 in the Saccharomyces cerevisiae tRNA Ile IAU anticodon stem and loop domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function of s 2 C at position 32 is a generalizable property. X-ray crystal structures of variously modified ASL Arg1 ICG and ASL Arg2 ICG constructs bound to cognate and wobble codons on the ribosome revealed the disruption of a C 32- A 38 cross-loop interaction but failed to fully explain the means by which s 2 C 32 restricts I 34 wobbling. Computational studies revealed that the adoption of a spatially broad inosine-adenosine base pair at the wobble position of the codon cannot be maintained simultaneously with the canonical ASL U-turn motif. C 32- A 38 cross-loop interactions are required for stability of the anticodon/codon interaction in the ribosomal A-site.


    Organizational Affiliation

    Department of Biological Sciences, University at Albany-SUNY, 1400 Washington Ave., Albany, NY, 12222, USA; The RNA Institute, University at Albany-SUNY, 1400 Washington Ave., Albany, NY, 12222, USA. Electronic address: paul.agris@duke.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7G156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10J105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12L132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15O89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19S93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein ThxV27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1507Thermus thermophilus HB8
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  • Entity ID: 22
    MoleculeChainsLengthOrganismImage
    tRNA ASL Escherichia coli Arg2X17Escherichia coli
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    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      mRNA A-site fragmentW6Escherichia coli
      Small Molecules
      Ligands 2 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
      MG
      Query on MG

      Download CCD File 
      A, E, J
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.46 Å
      • R-Value Free: 0.234 
      • R-Value Work: 0.203 
      • R-Value Observed: 0.203 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 403.73α = 90
      b = 403.73β = 90
      c = 177.42γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      PDB_EXTRACTdata extraction
      XDSdata reduction
      XSCALEdata scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States2RO1GM23037-25
      National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM110588-01
      National Science Foundation (NSF, United States)United StatesMCB1101859
      National Science Foundation (NSF, United States)United StatesCHE1407042

      Revision History 

      • Version 1.0: 2019-04-24
        Type: Initial release
      • Version 1.1: 2019-11-27
        Changes: Author supporting evidence
      • Version 1.2: 2020-01-29
        Changes: Database references
      • Version 1.3: 2020-03-11
        Changes: Database references, Refinement description, Source and taxonomy, Structure summary