3JCE

Structure of Escherichia coli EF4 in pretranslocational ribosomes (Pre EF4)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome

Zhang, D.Yan, K.Liu, G.Song, G.Luo, J.Shi, Y.Cheng, E.Wu, S.Jiang, T.Lou, J.Gao, N.Qin, Y.

(2016) Nat Struct Mol Biol 23: 125-131

  • DOI: 10.1038/nsmb.3160
  • Primary Citation of Related Structures:  
    3JCD, 3JCE

  • PubMed Abstract: 
  • EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted ...

    EF4 catalyzes tRNA back-translocation through an unknown mechanism. We report cryo-EM structures of Escherichia coli EF4 in post- and pretranslocational ribosomes (Post- and Pre-EF4) at 3.7- and 3.2-Å resolution, respectively. In Post-EF4, peptidyl-tRNA occupies the peptidyl (P) site, but the interaction between its CCA end and the P loop is disrupted. In Pre-EF4, the peptidyl-tRNA assumes a unique position near the aminoacyl (A) site, denoted the A site/EF4 bound (A/4) site, with a large displacement at its acceptor arm. Mutagenesis analyses suggest that a specific region in the EF4 C-terminal domain (CTD) interferes with base-pairing between the peptidyl-tRNA 3'-CCA and the P loop, whereas the EF4 CTD enhances peptidyl-tRNA interaction at the A/4 site. Therefore, EF4 induces back-translocation by disengaging the tRNA's CCA end from the peptidyl transferase center of the translating ribosome.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, China.



Macromolecules

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Entity ID: 2
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30S ribosomal protein S3B [auth c]233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 3
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30S ribosomal protein S4C [auth d]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 e]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 5
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30S ribosomal protein S6E [auth f]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 6
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30S ribosomal protein S7F [auth g]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 7
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30S ribosomal protein S8G [auth h]130Escherichia coli K-12Mutation(s): 0 
Gene Names: b3306JW3268rpsH
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Entity ID: 8
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30S ribosomal protein S9H [auth i]130Escherichia coli K-12Mutation(s): 0 
Gene Names: b3230JW3199rpsI
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30S ribosomal protein S10I [auth j]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11J [auth k]129Escherichia coli K-12Mutation(s): 0 
Gene Names: b3297JW3259rpsK
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30S ribosomal protein S12K [auth l]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 12
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30S ribosomal protein S13L [auth m]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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30S ribosomal protein S14M [auth n]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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30S ribosomal protein S15N [auth o]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 15
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30S ribosomal protein S16O [auth p]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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30S ribosomal protein S17P [auth q]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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30S ribosomal protein S18Q [auth r]75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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30S ribosomal protein S19R [auth s]92Escherichia coli K-12Mutation(s): 0 
Gene Names: b3316JW3278rpsS
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30S ribosomal protein S20S [auth t]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21T [auth u]71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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30S ribosomal protein S2U [auth b]241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 22
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50S ribosomal protein L32V [auth 0]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 23
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50S ribosomal protein L33W [auth 1]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34X [auth 2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35Y [auth 3]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 26
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50S ribosomal protein L36Z [auth 4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 27
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50S ribosomal protein L1AA [auth 5]234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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Entity ID: 30
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50S ribosomal protein L2DA [auth C]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 31
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50S ribosomal protein L3EA [auth D]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 32
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50S ribosomal protein L4FA [auth E]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 33
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50S ribosomal protein L5GA [auth F]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 34
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50S ribosomal protein L6HA [auth G]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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50S ribosomal protein L9IA [auth H]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 36
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50S ribosomal protein L11JA [auth I]142Escherichia coli K-12Mutation(s): 0 
Gene Names: b3983JW3946relCrplK
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50S ribosomal protein L13KA [auth J]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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50S ribosomal protein L14LA [auth K]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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50S ribosomal protein L15MA [auth L]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 40
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50S ribosomal protein L16NA [auth M]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 41
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50S ribosomal protein L17OA [auth N]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 42
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50S ribosomal protein L18PA [auth O]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19QA [auth P]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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50S ribosomal protein L20RA [auth Q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21SA [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22TA [auth S]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23UA [auth T]100Escherichia coli K-12Mutation(s): 0 
Gene Names: b3318JW3280rplW
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50S ribosomal protein L24VA [auth U]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25WA [auth V]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L27XA [auth W]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 51
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50S ribosomal protein L28YA [auth X]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 52
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50S ribosomal protein L29ZA [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 53
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50S ribosomal protein L30AB [auth Z]59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 57
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Elongation factor 4EB [auth x]599Escherichia coli K-12Mutation(s): 0 
Gene Names: lepAb2569JW2553
EC: 3.6.5.1 (PDB Primary Data), 3.6.5 (UniProt)
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16S ribosomal RNAA [auth a]1533Escherichia coli K-12
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23 ribosomal RNABA [auth A]2904Escherichia coli K-12
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5S ribosomal RNACA [auth B]120Escherichia coli K-12
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Entity ID: 54
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tRNABB [auth 6]76synthetic construct
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 55
    MoleculeChainsLengthOrganismImage
    mRNACB [auth 7]15synthetic construct
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 56
    MoleculeChainsLengthOrganismImage
    tRNADB [auth 8]77synthetic construct
    Protein Feature View
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    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 58
    MoleculeChainsLengthOrganismImage
    tRNAFB [auth 9]76synthetic construct
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GNP (Subject of Investigation/LOI)
    Query on GNP

    Download Ideal Coordinates CCD File 
    GB [auth x]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
    C10 H17 N6 O13 P3
    UQABYHGXWYXDTK-UUOKFMHZSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    HB [auth x]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.20 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: 2016-01-13
      Type: Initial release
    • Version 1.1: 2016-01-27
      Changes: Database references
    • Version 1.2: 2016-04-20
      Changes: Structure summary
    • Version 1.3: 2017-02-22
      Changes: Database references
    • Version 1.4: 2019-12-11
      Changes: Advisory, Data collection, Database references, Derived calculations
    • Version 2.0: 2019-12-18
      Changes: Advisory, Atomic model, Data collection, Derived calculations