4V5Q

The crystal structure of EF-Tu and G24A-tRNA-Trp bound to a near- cognate codon on the 70S ribosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

How Mutations in tRNA Distant from the Anticodon Affect the Fidelity of Decoding.

Schmeing, T.M.Voorhees, R.M.Kelley, A.C.Ramakrishnan, V.

(2011) Nat Struct Mol Biol 18: 432

  • DOI: 10.1038/nsmb.2003
  • Primary Citation of Related Structures:  
    4V5P, 4V5Q, 4V5R, 4V5S

  • PubMed Abstract: 
  • The ribosome converts genetic information into protein by selecting aminoacyl tRNAs whose anticodons base-pair to an mRNA codon. Mutations in the tRNA body can perturb this process and affect fidelity. The Hirsh suppressor is a well-studied tRNA(Trp) harboring a G24A mutation that allows readthrough of UGA stop codons ...

    The ribosome converts genetic information into protein by selecting aminoacyl tRNAs whose anticodons base-pair to an mRNA codon. Mutations in the tRNA body can perturb this process and affect fidelity. The Hirsh suppressor is a well-studied tRNA(Trp) harboring a G24A mutation that allows readthrough of UGA stop codons. Here we present crystal structures of the 70S ribosome complexed with EF-Tu and aminoacyl tRNA (native tRNA(Trp), G24A tRNA(Trp) or the miscoding A9C tRNA(Trp)) bound to cognate UGG or near-cognate UGA codons, determined at 3.2-Å resolution. The A9C and G24A mutations lead to miscoding by facilitating the distortion of tRNA required for decoding. A9C accomplishes this by increasing tRNA flexibility, whereas G24A allows the formation of an additional hydrogen bond that stabilizes the distortion. Our results also suggest that each native tRNA will adopt a unique conformation when delivered to the ribosome that allows accurate decoding.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK. martin.schmeing@mcgill.ca



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2 ABCB256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
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Entity ID: 3
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30S RIBOSOMAL PROTEIN S3 ACCC239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4 ADCD209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
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Entity ID: 5
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30S RIBOSOMAL PROTEIN S5 AECE162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6 AFCF101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
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Entity ID: 7
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30S RIBOSOMAL PROTEIN S7 AGCG156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
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Entity ID: 8
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30S RIBOSOMAL PROTEIN S8 AHCH138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
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Entity ID: 9
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30S RIBOSOMAL PROTEIN S9 AICI128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
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Entity ID: 10
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30S RIBOSOMAL PROTEIN S10 AJCJ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
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Entity ID: 11
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30S RIBOSOMAL PROTEIN S11 AKCK129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
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Entity ID: 12
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30S RIBOSOMAL PROTEIN S12 ALCL132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsLTTHA1697
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Entity ID: 13
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30S RIBOSOMAL PROTEIN S13 AMCM126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
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Entity ID: 14
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30S RIBOSOMAL PROTEIN S14 ANCN61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
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30S RIBOSOMAL PROTEIN S15 AOCO89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
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Entity ID: 16
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30S RIBOSOMAL PROTEIN S16 APCP88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
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30S RIBOSOMAL PROTEIN S17 AQCQ105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
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Entity ID: 18
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30S RIBOSOMAL PROTEIN S18 ARCR88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
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Entity ID: 19
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30S RIBOSOMAL PROTEIN S19 ASCS93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
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Entity ID: 20
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30S RIBOSOMAL PROTEIN S20 ATCT106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
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Entity ID: 21
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30S RIBOSOMAL PROTEIN THX AUCU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGATION FACTOR TU AZCZ405Thermus thermophilus HB8Mutation(s): 0 
Gene Names: tufAtufTTHA1694
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Entity ID: 26
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50S RIBOSOMAL PROTEIN L27 B0D085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmATTHA1782
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Entity ID: 27
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50S RIBOSOMAL PROTEIN L28 B1D198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmBTTHA0042
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Entity ID: 28
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50S RIBOSOMAL PROTEIN L29 B2D272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmCTTHA1684
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Entity ID: 29
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50S RIBOSOMAL PROTEIN L30 B3D360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmDTTHA1674
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Entity ID: 30
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50S RIBOSOMAL PROTEIN L31 B4D471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmETTHA1073
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Entity ID: 31
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50S RIBOSOMAL PROTEIN L32 B5D560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmFrpl32TTHA0418
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Entity ID: 32
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50S RIBOSOMAL PROTEIN L33 B6D654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmGrpl33TTHA0250
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34 B7D749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmHrpl34TTHA0446
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35 B8D865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmITTHA0552
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Entity ID: 35
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50S RIBOSOMAL PROTEIN L36 B9D937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJTTHA1668
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Entity ID: 38
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50S RIBOSOMAL PROTEIN L1 BCDC229Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 39
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50S RIBOSOMAL PROTEIN L2 BDDD276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplBTTHA1689
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Entity ID: 40
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50S RIBOSOMAL PROTEIN L3 BEDE206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplCTTHA1692
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Entity ID: 41
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50S RIBOSOMAL PROTEIN L4 BFDF210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplDTTHA1691
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Entity ID: 42
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50S RIBOSOMAL PROTEIN L5 BGDG182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplETTHA1680
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Entity ID: 43
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50S RIBOSOMAL PROTEIN L6 BHDH180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplFTTHA1677
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Entity ID: 44
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50S RIBOSOMAL PROTEIN L10 BJDJ173Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
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50S RIBOSOMAL PROTEIN L11 BKDK147Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
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50S RIBOSOMAL PROTEIN L13 BNDN140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplMTTHA1465
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Entity ID: 47
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50S RIBOSOMAL PROTEIN L14 BODO122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplNTTHA1682
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Entity ID: 48
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50S RIBOSOMAL PROTEIN L15 BPDP150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplOTTHA1673
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Entity ID: 49
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50S RIBOSOMAL PROTEIN L16 BQDQ141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplPTTHA1685
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Entity ID: 50
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50S RIBOSOMAL PROTEIN L17 BRDR118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQrpl17TTHA1663
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Entity ID: 51
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50S RIBOSOMAL PROTEIN L18 BSDS112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplRTTHA1676
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Entity ID: 52
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50S RIBOSOMAL PROTEIN L19 BTDT146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplSTTHA1031
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Entity ID: 53
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50S RIBOSOMAL PROTEIN L20 BUDU118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplTTTHA0553
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Entity ID: 54
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50S RIBOSOMAL PROTEIN L21 BVDV101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplUTTHA1783
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Entity ID: 55
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50S RIBOSOMAL PROTEIN L22 BWDW113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplVTTHA1687
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Entity ID: 56
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50S RIBOSOMAL PROTEIN L23 BXDX96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplWTTHA1690
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Entity ID: 57
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50S RIBOSOMAL PROTEIN L24 BYDY110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplXTTHA1681
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Entity ID: 58
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50S RIBOSOMAL PROTEIN L25 BZDZ206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplYrpl25rptL5TTHA1589
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S RRNAAA, CA1522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChainsLengthOrganismImage
E-SITE TRNA PHE OR P-SITE TRNA PHEAV, AW, CV, CW76Escherichia coli K-12
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Entity ID: 23
MoleculeChainsLengthOrganismImage
MRNAAX, CX27Escherichia coli
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Entity ID: 24
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A-SITE TRNA G24A TRP-TRNA TRPAY, CY77Escherichia coli K-12
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Entity ID: 36
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNABA, DA2915Thermus thermophilus HB8
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Entity ID: 37
MoleculeChainsLengthOrganismImage
5S RIBOSOMAL RNABB, DB122Thermus thermophilus HB8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 289.9α = 90
b = 269.4β = 91.51
c = 404.5γ = 90
Software Package:
Software NamePurpose
CNSmodel building
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

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 1.2: 2018-11-21
    Changes: Advisory, Data collection
  • Version 2.0: 2019-06-26
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-10-30
    Changes: Advisory, Data collection, Derived calculations