2UXB

Crystal structure of an extended tRNA anticodon stem loop in complex with its cognate mRNA GGGU in the context of the Thermus thermophilus 30S subunit.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.295 
  • R-Value Observed: 0.295 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structures of tRNAs with an expanded anticodon loop in the decoding center of the 30S ribosomal subunit.

Dunham, C.M.Selmer, M.Phelps, S.S.Kelley, A.C.Suzuki, T.Joseph, S.Ramakrishnan, V.

(2007) RNA 13: 817-823

  • DOI: 10.1261/rna.367307
  • Primary Citation of Related Structures:  
    2UXB, 2UXC, 2UXD

  • PubMed Abstract: 
  • During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we repor ...

    During translation, some +1 frameshift mRNA sites are decoded by frameshift suppressor tRNAs that contain an extra base in their anticodon loops. Similarly engineered tRNAs have been used to insert nonnatural amino acids into proteins. Here, we report crystal structures of two anticodon stem-loops (ASLs) from tRNAs known to facilitate +1 frameshifting bound to the 30S ribosomal subunit with their cognate mRNAs. ASL(CCCG) and ASL(ACCC) (5'-3' nomenclature) form unpredicted anticodon-codon interactions where the anticodon base 34 at the wobble position contacts either the fourth codon base or the third and fourth codon bases. In addition, we report the structure of ASL(ACGA) bound to the 30S ribosomal subunit with its cognate mRNA. The tRNA containing this ASL was previously shown to be unable to facilitate +1 frameshifting in competition with normal tRNAs (Hohsaka et al. 2001), and interestingly, it displays a normal anticodon-codon interaction. These structures show that the expanded anticodon loop of +1 frameshift promoting tRNAs are flexible enough to adopt conformations that allow three bases of the anticodon to span four bases of the mRNA. Therefore it appears that normal triplet pairing is not an absolute constraint of the decoding center.


    Organizational Affiliation

    MRC-Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
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
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
RIBOSOMAL PROTEIN S4D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
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
RIBOSOMAL PROTEIN S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
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
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
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RIBOSOMAL PROTEIN S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 10
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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
RIBOSOMAL PROTEIN S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S12L135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 13
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RIBOSOMAL PROTEIN S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN S14N61Thermus 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
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
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
RIBOSOMAL PROTEIN S17Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
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
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
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
RIBOSOMAL PROTEIN THXU27Thermus 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 RIBOSOMAL RNAA1522Thermus thermophilus HB8
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  • Entity ID: 22
    MoleculeChainsLengthOrganismImage
    A-SITE MESSENGER RNA FRAGMENT GGGUX4synthetic construct
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    • Entity ID: 23
      MoleculeChainsLengthOrganismImage
      ANTICODON STEM-LOOP OF TRANSFER RNA WITH ANTICODON ACCCY18synthetic construct
      Small Molecules
      Ligands 4 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 
      G
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      K
      Query on K

      Download CCD File 
      G
      POTASSIUM ION
      K
      NPYPAHLBTDXSSS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download CCD File 
      G
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.10 Å
      • R-Value Free: 0.328 
      • R-Value Work: 0.295 
      • R-Value Observed: 0.295 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 401.95α = 90
      b = 401.95β = 90
      c = 174.086γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      XDSdata reduction
      XDSdata scaling
      CNSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2007-07-31
        Type: Initial release
      • Version 1.1: 2012-09-19
        Changes: Atomic model, Derived calculations, Non-polymer description, Other, Version format compliance
      • Version 1.2: 2012-10-10
        Changes: Derived calculations
      • Version 1.3: 2013-12-25
        Changes: Derived calculations, Other
      • Version 2.0: 2018-03-14
        Changes: Advisory, Atomic model, Database references, Source and taxonomy
      • Version 2.1: 2019-01-30
        Changes: Data collection, Database references, Experimental preparation
      • Version 2.2: 2019-03-06
        Changes: Data collection, Experimental preparation