6MPF

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a 2-thiocytidine (s2C32) and inosine (I34) modified anticodon stem loop (ASL) of Escherichia coli transfer RNA Arginine 1 (TRNAARG1) bound to an mRNA with an CGC-codon in the A-site and paromomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 2.1 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:  
    6DTI, 6MKN, 6MPI, 6MPF

  • 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-methyladenosine modifications at positions 34 (I 34 ) and 37 (m 2 A 37 ) ...

    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 S2 B234Thermus 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 S3 C206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4 D208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5 E150Thermus 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 S6 F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7 G155Thermus 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 S8 H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9 I127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S10 J98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S11 K119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12 L124Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S13 M125Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14 type Z N60Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15 O88Thermus 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 S16 P83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17 Q104Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18 R73Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19 S80Thermus 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 S20 T99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein Thx V24Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1508Thermus thermophilus HB8
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  • Entity ID: 22
    MoleculeChainsLengthOrganismImage
    mRNA A-site fragmentW4Escherichia coli
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    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      tRNA ASL Escherichia coli Arg1X11Escherichia coli
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      PAR
      Query on PAR

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

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

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      A, E, J, W, X
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.33 Å
      • R-Value Free: 0.219 
      • R-Value Work: 0.178 
      • R-Value Observed: 0.178 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 402.33α = 90
      b = 402.33β = 90
      c = 176.03γ = 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  (Full details and data files)

      • Version 1.0: 2019-04-24
        Type: Initial release
      • Version 1.1: 2019-11-27
        Changes: Author supporting evidence
      • Version 2.0: 2020-01-29
        Changes: Data collection, Database references, Polymer sequence
      • Version 2.1: 2020-03-11
        Changes: Database references