4V6L

Structural insights into cognate vs. near-cognate discrimination during decoding.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history


Literature

Structural insights into cognate versus near-cognate discrimination during decoding.

Agirrezabala, X.Schreiner, E.Trabuco, L.G.Lei, J.Ortiz-Meoz, R.F.Schulten, K.Green, R.Frank, J.

(2011) EMBO J 30: 1497-1507

  • DOI: 10.1038/emboj.2011.58
  • Primary Citation of Related Structures:  
    4V6L, 4V6K

  • PubMed Abstract: 
  • The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Go ...

    The structural basis of the tRNA selection process is investigated by cryo-electron microscopy of ribosomes programmed with UGA codons and incubated with ternary complex (TC) containing the near-cognate Trp-tRNA(Trp) in the presence of kirromycin. Going through more than 350 000 images and employing image classification procedures, we find ∼8% in which the TC is bound to the ribosome. The reconstructed 3D map provides a means to characterize the arrangement of the near-cognate aa-tRNA with respect to elongation factor Tu (EF-Tu) and the ribosome, as well as the domain movements of the ribosome. One of the interesting findings is that near-cognate tRNA's acceptor stem region is flexible and CCA end becomes disordered. The data bring direct structural insights into the induced-fit mechanism of decoding by the ribosome, as the analysis of the interactions between small and large ribosomal subunit, aa-tRNA and EF-Tu and comparison with the cognate case (UGG codon) offers clues on how the conformational signals conveyed to the GTPase differ in the two cases.


    Organizational Affiliation

    Structural Biology Unit, CIC-bioGUNE, Derio, Basque Country, Spain.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor Tu 2AC393Escherichia coli K-12Mutation(s): 0 
Gene Names: tufBb3980JW3943
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Entity ID: 5
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30S ribosomal protein S2AF241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S3AG233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4AH206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5AI167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6AJ135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 10
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30S ribosomal protein S7AK179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 11
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30S ribosomal protein S8AL130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 12
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30S ribosomal protein S9AM130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 13
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30S ribosomal protein S10AN103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 14
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30S ribosomal protein S11AO129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 15
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30S ribosomal protein S12AP124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 16
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30S ribosomal protein S13AQ118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 17
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30S ribosomal protein S14AR101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 18
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30S ribosomal protein S15AS89Escherichia coli O157:H7Mutation(s): 0 
Gene Names: rpsOZ4526ECs4046
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Entity ID: 19
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30S ribosomal protein S16AT82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 20
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30S ribosomal protein S17AU84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 21
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30S ribosomal protein S18AV75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 22
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30S ribosomal protein S19AW92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 23
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30S ribosomal protein S20AX87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 24
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30S ribosomal protein S21AY71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 27
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50S ribosomal protein L1BC234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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Entity ID: 28
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50S ribosomal protein L2BD273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 29
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50S ribosomal protein L3BE209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 30
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50S ribosomal protein L4BF201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 31
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50S ribosomal protein L5BG179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 32
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50S ribosomal protein L6BH177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 33
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50S ribosomal protein L9BI149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 34
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50S ribosomal protein L11BJ142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 35
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50S ribosomal protein L13BK142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 36
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50S ribosomal protein L14BL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 37
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50S ribosomal protein L15BM144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 38
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50S ribosomal protein L16BN136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 39
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50S ribosomal protein L17BO127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 40
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50S ribosomal protein L18BP117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 41
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50S ribosomal protein L19BQ115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 42
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50S ribosomal protein L20BR118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 43
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50S ribosomal protein L21BS103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 44
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50S ribosomal protein L22BT110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 45
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50S ribosomal protein L23BU100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 46
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50S ribosomal protein L24BV104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 47
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50S ribosomal protein L25BW94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 48
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50S ribosomal protein L27BX85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 49
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50S ribosomal protein L28BY78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 50
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50S ribosomal protein L29BZ63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 51
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50S ribosomal protein L30Ba59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 52
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50S ribosomal protein L31Bb70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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Entity ID: 53
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50S ribosomal protein L32Bc57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 54
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50S ribosomal protein L33Bd55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 55
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50S ribosomal protein L34Be46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 56
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50S ribosomal protein L35Bf65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 57
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50S ribosomal protein L36Bg38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
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16S ribosomal RNAAA1542Escherichia coli DH1
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Entity ID: 2
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A/T-site tRNA PheAB, AE76Escherichia coli DH1
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Entity ID: 4
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mRNAAD24Escherichia coli
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Entity ID: 25
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50S ribosomal RNA 5SBA120Escherichia coli K-12
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Entity ID: 26
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50S ribosomal RNA 23SBB2904Escherichia coli K-12
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 13.2 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-25
    Changes: Other
  • Version 2.0: 2018-07-18
    Changes: Data collection, Polymer sequence
  • Version 3.0: 2019-07-03
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2019-12-18
    Changes: Other