3JCD

Structure of Escherichia coli EF4 in posttranslocational ribosomes (Post EF4)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 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: https://doi.org/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. 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

    Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2A [auth b]241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3B [auth c]233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsC
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4C [auth d]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth e]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6E [auth f]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth g]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth h]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth i]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth j]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth k]129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12K [auth l]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13L [auth m]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14M [auth n]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth o]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth p]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth q]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18Q [auth r]75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsR
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19R [auth s]92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth t]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21T [auth u]71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsU
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32U [auth 0]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33V [auth 1]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmG
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34W [auth 2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmH
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35X [auth 3]64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmI
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36Y [auth 4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L1Z [auth 5]234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplAb3984JW3947
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth C]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth D]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth E]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplD
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5DA [auth F]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth G]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth H]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11GA [auth I]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth J]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth K]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth L]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16KA [auth M]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17LA [auth N]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18MA [auth O]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19NA [auth P]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20OA [auth Q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplT
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21PA [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22QA [auth S]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23RA [auth T]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24SA [auth U]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25TA [auth V]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27UA [auth W]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28VA [auth X]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth Z]59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 4YA [auth x]599Escherichia coli K-12Mutation(s): 0 
Gene Names: lepAb2569JW2553
EC: 3.6.5.1
UniProt
Find proteins for P60785 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains LengthOrganismImage
16S ribosomal RNAZA [auth a]1,533Escherichia coli K-12
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Entity ID: 53
MoleculeChains LengthOrganismImage
23S ribosomal RNAAB [auth A]2,904Escherichia coli K-12
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Entity ID: 54
MoleculeChains LengthOrganismImage
5S ribosomal RNABB [auth B]120Escherichia coli K-12
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Entity ID: 55
MoleculeChains LengthOrganismImage
mRNACB [auth 7]15synthetic construct
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNADB [auth 8],
EB [auth 9]
76synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2018-10-17
    Changes: Data collection, Database references, Structure summary
  • Version 1.5: 2019-12-18
    Changes: Advisory, Derived calculations