4V77

E. coli 70S-fMetVal-tRNAVal-tRNAfMet complex in intermediate post-translocation state (post2b)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 17.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Energy barriers and driving forces in tRNA translocation through the ribosome.

Bock, L.V.Blau, C.Schroder, G.F.Davydov, I.I.Fischer, N.Stark, H.Rodnina, M.V.Vaiana, A.C.Grubmuller, H.

(2013) Nat Struct Mol Biol 20: 1390-1396

  • DOI: 10.1038/nsmb.2690
  • Primary Citation of Related Structures:  
    4V6Y, 4V6Z, 4V70, 4V71, 4V72, 4V73, 4V74, 4V75, 4V76, 4V77, 4V78, 4V79, 4V7A

  • PubMed Abstract: 
  • During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data ...

    During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM data. Resolving fast transitions between states, we find that tRNA motions govern the transition rates within the pre- and post-translocation states. Intersubunit rotations and L1-stalk motion exhibit fast intrinsic submicrosecond dynamics. The L1 stalk drives the tRNA from the peptidyl site and links intersubunit rotation to translocation. Displacement of tRNAs is controlled by 'sliding' and 'stepping' mechanisms involving conserved L16, L5 and L1 residues, thus ensuring binding to the ribosome despite large-scale tRNA movement. Our results complement structural data with a time axis, intrinsic transition rates and molecular forces, revealing correlated functional motions inaccessible by other means.


    Organizational Affiliation

    1] Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. [2].



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2A [auth AB]220Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsBb0169JW0164
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Entity ID: 2
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30S ribosomal protein S3B [auth AC]208Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsCb3314JW3276
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Entity ID: 3
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30S ribosomal protein S4C [auth AD]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 4
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30S ribosomal protein S5D [auth AE]152Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 5
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30S ribosomal protein S6E [auth AF]101Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsFb4200JW4158
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Entity ID: 6
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30S ribosomal protein S7F [auth AG]152Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsGb3341JW3303
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Entity ID: 7
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30S ribosomal protein S8G [auth AH]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9H [auth AI]128Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsIb3230JW3199
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30S ribosomal protein S10I [auth AJ]100Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11J [auth AK]118Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsKb3297JW3259
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30S ribosomal protein S12K [auth AL]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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30S ribosomal protein S13L [auth AM]115Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsMb3298JW3260
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30S ribosomal protein S14M [auth AN]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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30S ribosomal protein S15N [auth AO]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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30S ribosomal protein S16O [auth AP]81Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsPb2609JW2590
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30S ribosomal protein S17P [auth AQ]82Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsQneaAb3311JW3273
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30S ribosomal protein S18Q [auth AR]57Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsRb4202JW4160
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30S ribosomal protein S19R [auth AS]81Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsSb3316JW3278
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30S ribosomal protein S20S [auth AT]86Escherichia coli K-12Mutation(s): 1 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21T [auth AU]53Escherichia coli K-12Mutation(s): 2 
Gene Names: rpsUb3065JW3037
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Entity ID: 25
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50S ribosomal protein L2Y [auth BC]273Escherichia coli K-12Mutation(s): 1 
Gene Names: rplBb3317JW3279
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Entity ID: 26
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50S ribosomal protein L3Z [auth BD]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L4AA [auth BE]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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50S ribosomal protein L5BA [auth BF]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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50S ribosomal protein L6CA [auth BG]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 30
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50S ribosomal protein L9DA [auth BH]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 31
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50S ribosomal protein L11EA [auth BI]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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50S ribosomal protein L13FA [auth BJ]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 33
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50S ribosomal protein L14GA [auth BK]123Escherichia coli K-12Mutation(s): 1 
Gene Names: rplNb3310JW3272
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Entity ID: 34
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50S ribosomal protein L15HA [auth BL]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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50S ribosomal protein L16IA [auth BM]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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50S ribosomal protein L17JA [auth BN]121Escherichia coli K-12Mutation(s): 1 
Gene Names: rplQb3294JW3256
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50S ribosomal protein L18KA [auth BO]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19LA [auth BP]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 39
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50S ribosomal protein L20MA [auth BQ]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21NA [auth BR]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 41
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50S ribosomal protein L22OA [auth BS]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 42
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50S ribosomal protein L23PA [auth BT]94Escherichia coli K-12Mutation(s): 1 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24QA [auth BU]104Escherichia coli K-12Mutation(s): 1 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25RA [auth BV]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L27SA [auth BW]80Escherichia coli K-12Mutation(s): 1 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28TA [auth BX]79Escherichia coli K-12Mutation(s): 1 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29UA [auth BY]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L30VA [auth BZ]59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32WA [auth B0]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 50
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50S ribosomal protein L33XA [auth B1]52Escherichia coli K-12Mutation(s): 2 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34YA [auth B2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35ZA [auth B3]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 53
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50S ribosomal protein L36AB [auth B4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 56
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50S ribosomal protein L1DB [auth B5]234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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Entity ID: 21
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16S ribosomal RNAU [auth AA]1533Escherichia coli K-12
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Entity ID: 22
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fMet-Val-tRNA-ValV [auth A1]76Escherichia coli K-12
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  • Entity ID: 23
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    5'-R(*AP*CP*UP*AP*UP*GP*GP*UP*UP*UP*UP*UP*AP*UP*U)-3'W [auth A2]15N/A
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    Entity ID: 24
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    tRNA-fMetX [auth A3]77Escherichia coli K-12
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    Entity ID: 54
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    23S ribosomal RNABB [auth BA]2903Escherichia coli K-12
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    • Reference Sequence
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    Entity ID: 55
    MoleculeChainsLengthOrganismImage
    5S ribosomal RNACB [auth BB]118Escherichia coli K-12
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FME (Subject of Investigation/LOI)
    Query on FME

    Download Ideal Coordinates CCD File 
    FB [auth BA]N-FORMYLMETHIONINE
    C6 H11 N O3 S
    PYUSHNKNPOHWEZ-YFKPBYRVSA-N
     Ligand Interaction
    VAL
    Query on VAL

    Download Ideal Coordinates CCD File 
    EB [auth A1]VALINE
    C5 H11 N O2
    KZSNJWFQEVHDMF-BYPYZUCNSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 17.0 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    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: 2015-04-15
      Changes: Other
    • Version 2.0: 2018-07-18
      Changes: Data collection, Polymer sequence
    • Version 2.1: 2018-09-05
      Changes: Data collection, Experimental preparation, Refinement description
    • Version 2.2: 2019-12-18
      Changes: Database references, Derived calculations, Other