4V9I

Crystal structure of thermus thermophilus 70S in complex with tRNAs and mRNA containing a pseudouridine in a stop codon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Unusual base pairing during the decoding of a stop codon by the ribosome.

Fernandez, I.S.Ng, C.L.Kelley, A.C.Wu, G.Yu, Y.T.Ramakrishnan, V.

(2013) Nature 500: 107-110

  • DOI: 10.1038/nature12302
  • Primary Citation of Related Structures:  
    4K0K, 4V9I, 4JV5, 4JYA

  • PubMed Abstract: 
  • During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs ...

    During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Ψ) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs. Here we determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the ΨAG stop codon in the A site. The ΨA base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S2B [auth AB], HB [auth CB]234Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S3C [auth AC], IB [auth CC]206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S4D [auth AD], JB [auth CD]208Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S5E [auth AE], KB [auth CE]150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S6F [auth AF], LB [auth CF]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S7G [auth AG], MB [auth CG]155Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S8H [auth AH], NB [auth CH]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S9I [auth AI], OB [auth CI]127Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S10J [auth AJ], PB [auth CJ]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S11K [auth AK], QB [auth CK]119Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S12L [auth AL], RB [auth CL]124Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S13M [auth AM], SB [auth CM]124Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S14N [auth AN], TB [auth CN]60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S15O [auth AO], UB [auth CO]88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S16P [auth AP], VB [auth CP]83Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S17Q [auth AQ], WB [auth CQ]99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S18R [auth AR], XB [auth CR]70Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S19S [auth AS], YB [auth CS]78Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein S20T [auth AT], ZB [auth CT]99Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
30S Ribosomal protein THXU [auth AU], AC [auth CU]24Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L1BA [auth BC]206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2CA [auth BD], IC [auth DD]271Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3DA [auth BE], JC [auth DE]204Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4EA [auth BF], KC [auth DF]207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5FA [auth BG], LC [auth DG]181Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6GA [auth BH], MC [auth DH]159Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L9HA [auth BI], NC [auth DI]145Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplITTHA0242
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10IA [auth BJ], OC [auth DJ]130Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13JA [auth BN], PC [auth DN]138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
UniProt
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14KA [auth BO], QC [auth DO]122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15LA [auth BP], RC [auth DP]146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16MA [auth BQ], SC [auth DQ]141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17NA [auth BR], TC [auth DR]117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18OA [auth BS], UC [auth DS]98Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19PA [auth BT], VC [auth DT]137Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20QA [auth BU], WC [auth DU]117Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21RA [auth BV], XC [auth DV]101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22SA [auth BW], YC [auth DW]113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23TA [auth BX], ZC [auth DX]92Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24UA [auth BY], AD [auth DY]100Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25VA [auth BZ], BD [auth DZ]176Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27WA [auth B0], CD [auth D0]84Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28XA [auth B1], DD [auth D1]93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29YA [auth B2], ED [auth D2]71Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30ZA [auth B3], FD [auth D3]59Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31AB [auth B4], GD [auth D4]30Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32BB [auth B5], HD [auth D5]59Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33CB [auth B6], ID [auth D6]44Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34DB [auth B7], JD [auth D7]48Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35EB [auth B8], KD [auth D8]63Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
UniProt
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36FB [auth B9], LD [auth D9]36Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
UniProt
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
50S Ribosomal protein L1HC [auth DC]196Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S ribosomal RNAA [auth AA], GB [auth CA]1504Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
P-SITE tRNAV [auth AV], BC [auth CV]77Escherichia coli
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Entity ID: 23
MoleculeChainsLengthOrganismImage
E-SITE tRNAW [auth AW], CC [auth CW]76Escherichia coli
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Entity ID: 24
MoleculeChainsLengthOrganismImage
A-SITE tRNAX [auth AY], DC [auth CY]75Escherichia coli
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  • Entity ID: 25
    MoleculeChainsLengthOrganismImage
    mRNAY [auth AX]7synthetic construct
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    Entity ID: 26
    MoleculeChainsLengthOrganismImage
    23S ribosomal RNAZ [auth BA], FC [auth DA]2915Thermus thermophilus HB8
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    Entity ID: 27
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNAAA [auth BB], GC [auth DB]119Thermus thermophilus HB8
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    • Entity ID: 59
      MoleculeChainsLengthOrganismImage
      mRNAEC [auth CX]4synthetic construct
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      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.30 Å
      • R-Value Free: 0.279 
      • R-Value Work: 0.225 
      • R-Value Observed: 0.228 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 209.92α = 90
      b = 449.9β = 90
      c = 624.9γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      PDB_EXTRACTdata extraction
      ADSCdata collection
      MOLREPphasing
      XDSdata reduction
      XDSdata scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2014-07-09
        Type: Initial release
      • Version 1.1: 2014-12-10
        Changes: Other