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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 3.1 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: 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: rpsD
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5D [auth e]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsE
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, fully modified isoformE [auth f]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsF
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7F [auth g]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsG
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8G [auth h]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsH
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9H [auth i]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsI
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10I [auth j]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJ
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11J [auth k]129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsK
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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: rpsM
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14M [auth n]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsN
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15N [auth o]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsO
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16O [auth p]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsP
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17P [auth q]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQ
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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: rpsS
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20S [auth t]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsT
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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
30S ribosomal protein S2U [auth b]241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsB
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32V [auth 0]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmF
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33W [auth 1]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmG
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34X [auth 2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmH
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35Y [auth 3]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmI
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36Z [auth 4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJ
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1AA [auth 5]234Escherichia coli K-12Mutation(s): 0 
Gene Names: rplA
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2DA [auth C]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplB
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3EA [auth D]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplC
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4FA [auth E]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplD
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5GA [auth F]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplE
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6HA [auth G]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplF
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9IA [auth H]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplI
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11JA [auth I]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplK
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13KA [auth J]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplM
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14LA [auth K]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplN
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15MA [auth L]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplO
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16NA [auth M]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplP
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17OA [auth N]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQ
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PA [auth O]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplR
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19QA [auth P]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplS
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20RA [auth Q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplT
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21SA [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplU
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22TA [auth S]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplV
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23UA [auth T]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplW
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24VA [auth U]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplX
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25WA [auth V]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplY
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27XA [auth W]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmA
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28YA [auth X]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmB
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29ZA [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmC
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AB [auth Z]59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmD
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 4EB [auth x]599Escherichia coli K-12Mutation(s): 0 
Gene Names: lepA
EC: 3.6.5
UniProt
Find proteins for P60785 (Escherichia coli (strain K12))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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: 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
  • Version 3.0: 2023-08-02
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 3.1: 2024-06-05
    Changes: Data collection, Refinement description