5UYK

70S ribosome bound with cognate ternary complex not base-paired to A site codon (Structure I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Ensemble cryo-EM elucidates the mechanism of translation fidelity

Loveland, A.B.Demo, G.Grigorieff, N.Korostelev, A.A.

(2017) Nature 546: 113-117

  • DOI: 10.1038/nature22397
  • Primary Citation of Related Structures:  
    5UYQ, 5UYL, 5UYK, 5UYN, 5UYM, 5UYP

  • PubMed Abstract: 
  • Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-reso ...

    Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit. A transient conformation of decoding-centre nucleotide G530 stabilizes the cognate codon-anticodon helix, initiating step-wise 'latching' of the decoding centre. The resulting closure of the 30S subunit docks EF-Tu at the sarcin-ricin loop of the 50S subunit, activating EF-Tu for GTP hydrolysis and enabling accommodation of the aminoacyl-tRNA. By contrast, near-cognate complexes fail to induce the G530 latch, thus favouring open 30S pre-accommodation intermediates with inactive EF-Tu. This work reveals long-sought structural differences between the pre-accommodation of cognate and near-cognate tRNAs that elucidate the mechanism of accurate decoding.


    Organizational Affiliation

    RNA Therapeutics Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, Massachusetts 01605, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L204271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 2
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50S ribosomal protein L305209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 3
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50S ribosomal protein L406201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 4
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50S ribosomal protein L507177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L608176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L909149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 7
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50S ribosomal protein L1010131Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
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Entity ID: 8
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50S ribosomal protein L1111141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 9
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50S ribosomal protein L1312142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 10
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50S ribosomal protein L1413122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 11
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50S ribosomal protein L1514143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 12
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50S ribosomal protein L1615136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 13
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50S ribosomal protein L1716120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 14
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50S ribosomal protein L1817116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 15
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50S ribosomal protein L1918114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 16
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50S ribosomal protein L2019117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 17
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50S ribosomal protein L2120103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 18
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50S ribosomal protein L2221110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 19
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50S ribosomal protein L232293Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 20
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50S ribosomal protein L2423102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 21
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50S ribosomal protein L252494Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 22
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50S ribosomal protein L272575Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 23
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50S ribosomal protein L282677Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 24
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50S ribosomal protein L292763Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 25
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50S ribosomal protein L302858Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 26
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50S ribosomal protein L312966Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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Entity ID: 27
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50S ribosomal protein L323056Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L333150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L343246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L353364Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 31
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50S ribosomal protein L363438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3C206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4D205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 35
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30S ribosomal protein S5E157Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 36
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30S ribosomal protein S6F100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 37
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30S ribosomal protein S7G151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 38
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30S ribosomal protein S8H129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 39
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30S ribosomal protein S9I127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 40
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30S ribosomal protein S10J98Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 41
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30S ribosomal protein S11K116Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 42
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30S ribosomal protein S12L123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 43
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30S ribosomal protein S13M114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 44
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30S ribosomal protein S14N100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 45
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30S ribosomal protein S15O88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 46
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30S ribosomal protein S16P82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 47
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30S ribosomal protein S17Q80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 48
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30S ribosomal protein S18R65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 49
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30S ribosomal protein S19S79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 50
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30S ribosomal protein S20T85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 51
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30S ribosomal protein S21U65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
Find proteins for P68679 (Escherichia coli (strain K12))
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Entity ID: 52
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50S ribosomal protein L103223Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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Entity ID: 59
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Elongation factor Tu 2Z392Escherichia coli K-12Mutation(s): 0 
Gene Names: tufAb3339JW3301
Find proteins for P0CE47 (Escherichia coli (strain K12))
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Entity ID: 53
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16S ribosomal RNAA1539Escherichia coli K-12
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Entity ID: 54
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23S ribosomal RNA012903Escherichia coli K-12
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Entity ID: 55
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5S ribosomal RNA02120Escherichia coli K-12
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Entity ID: 56
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tRNAfMetW, X77Escherichia coli K-12
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  • Entity ID: 57
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    mRNAV20Escherichia coli K-12
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    Entity ID: 58
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    tRNAPheY76Escherichia coli K-12
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GCP
    Query on GCP

    Download CCD File 
    Z
    PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
    C11 H18 N5 O13 P3
    PHBDHXOBFUBCJD-KQYNXXCUSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    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 StatesR01 GM106105
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM107465
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01 GM62580
    Howard Hughes Medical Institute (HHMI)United StatesHoward Hughes Medical Institute Post-Doctoral Fellow of Helen Hay Whitney Foundation

    Revision History 

    • Version 1.0: 2017-06-07
      Type: Initial release
    • Version 1.1: 2017-09-13
      Changes: Author supporting evidence, Data collection
    • Version 1.2: 2018-07-18
      Changes: Data collection, Experimental preparation
    • Version 1.3: 2019-11-20
      Changes: Author supporting evidence