4V8Q

Complex of SmpB, a tmRNA fragment and EF-Tu-GDP-Kirromycin with the 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Decoding in the absence of a codon by tmRNA and SmpB in the ribosome.

Neubauer, C.Gillet, R.Kelley, A.C.Ramakrishnan, V.

(2012) Science 335: 1366-1369

  • DOI: 10.1126/science.1217039
  • Primary Citation of Related Structures:  
    4V8Q

  • PubMed Abstract: 
  • In bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger RNA (tmRNA), a bifunctional molecule that acts as both a transfer RNA (tRNA) and a messenger RNA (mRNA), and SmpB, a small protein that works in concert with tmRNA ...

    In bacteria, ribosomes stalled at the end of truncated messages are rescued by transfer-messenger RNA (tmRNA), a bifunctional molecule that acts as both a transfer RNA (tRNA) and a messenger RNA (mRNA), and SmpB, a small protein that works in concert with tmRNA. Here, we present the crystal structure of a tmRNA fragment, SmpB and elongation factor Tu bound to the ribosome at 3.2 angstroms resolution. The structure shows how SmpB plays the role of both the anticodon loop of tRNA and portions of mRNA to facilitate decoding in the absence of an mRNA codon in the A site of the ribosome and explains why the tmRNA-SmpB system does not interfere with normal translation.


    Organizational Affiliation

    Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge, UK.



Macromolecules

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50S RIBOSOMAL PROTEIN L27 A085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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50S RIBOSOMAL PROTEIN L28 A198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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50S RIBOSOMAL PROTEIN L29 A272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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50S RIBOSOMAL PROTEIN L30 A360Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L31 A471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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50S RIBOSOMAL PROTEIN L32 A560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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50S RIBOSOMAL PROTEIN L33 A654Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L34 A749Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L35 A865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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50S RIBOSOMAL PROTEIN L36 A937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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50S RIBOSOMAL PROTEIN L1 AC229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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50S RIBOSOMAL PROTEIN L2 AD276Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L3 AE206Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L4 AF210Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L5 AG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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50S RIBOSOMAL PROTEIN L6 AH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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50S RIBOSOMAL PROTEIN L10 AJ130Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L11 AK140Thermus thermophilus HB8Mutation(s): 0 
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50S RIBOSOMAL PROTEIN L13 AN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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50S RIBOSOMAL PROTEIN L14 AO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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50S RIBOSOMAL PROTEIN L15 AP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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50S RIBOSOMAL PROTEIN L16 AQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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50S RIBOSOMAL PROTEIN L17 AR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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50S RIBOSOMAL PROTEIN L18 AS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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50S RIBOSOMAL PROTEIN L19 AT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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50S RIBOSOMAL PROTEIN L20 AU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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50S RIBOSOMAL PROTEIN L21 AV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L22 AW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L23 AX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L24 AY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 33
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50S RIBOSOMAL PROTEIN L25 AZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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Entity ID: 34
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SMALL PROTEIN B SMPB B2144Thermus thermophilus HB8Mutation(s): 0 
Gene Names: smpBTTHA0902
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Entity ID: 36
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30S RIBOSOMAL PROTEIN S2 BB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 37
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30S RIBOSOMAL PROTEIN S3 BC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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30S RIBOSOMAL PROTEIN S4 BD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 39
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30S RIBOSOMAL PROTEIN S5 BE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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30S RIBOSOMAL PROTEIN S6 BF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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30S RIBOSOMAL PROTEIN S7 BG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 42
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30S RIBOSOMAL PROTEIN S8 BH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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30S RIBOSOMAL PROTEIN S9 BI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 44
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30S RIBOSOMAL PROTEIN S10 BJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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30S RIBOSOMAL PROTEIN S11 BK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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30S RIBOSOMAL PROTEIN S12 BL135Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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30S RIBOSOMAL PROTEIN S13 BM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 48
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30S RIBOSOMAL PROTEIN S14 BN61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
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30S RIBOSOMAL PROTEIN S15 BO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 50
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30S RIBOSOMAL PROTEIN S16 BP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 51
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30S RIBOSOMAL PROTEIN S17 BQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 52
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30S RIBOSOMAL PROTEIN S18 BR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 53
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30S RIBOSOMAL PROTEIN S19 BS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 54
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30S RIBOSOMAL PROTEIN S20 BT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 55
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30S RIBOSOMAL PROTEIN THX BU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 59
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ELONGATION FACTOR TU BZ405Thermus thermophilus HB8Mutation(s): 0 
Gene Names: tufAtufTTHA1694
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Entity ID: 11
MoleculeChainsLengthOrganismImage
23S ribosomal RNAAA2915Thermus thermophilus HB8
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Entity ID: 12
MoleculeChainsLengthOrganismImage
5S ribosomal RNAAB122Thermus thermophilus HB8
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Entity ID: 35
MoleculeChainsLengthOrganismImage
16S ribosomal RNABA1522Thermus thermophilus HB8
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Entity ID: 56
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E-SITE or P-SITE TRNA FMETBV, BW77Escherichia coli K-12
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  • Entity ID: 57
    MoleculeChainsLengthOrganismImage
    MRNABX19Escherichia coli
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    Entity ID: 58
    MoleculeChainsLengthOrganismImage
    TMRNA DELABY90Thermus thermophilus HB8
    Small Molecules
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.10 Å
    • R-Value Free: 0.270 
    • R-Value Work: 0.230 
    • R-Value Observed: 0.230 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 202.17α = 90
    b = 290.76β = 97.63
    c = 250.65γ = 90
    Software Package:
    Software NamePurpose
    PHASERmodel building
    CNSrefinement
    XDSdata reduction
    XDSdata scaling
    PHASERphasing

    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
    • Version 2.0: 2018-03-07
      Changes: Advisory, Atomic model, Database references, Source and taxonomy, Structure summary
    • Version 2.1: 2019-10-09
      Changes: Data collection, Derived calculations, Source and taxonomy
    • Version 2.2: 2019-10-30
      Changes: Advisory, Data collection, Derived calculations