3JBV

Mechanisms of Ribosome Stalling by SecM at Multiple Elongation Steps


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Mechanisms of ribosome stalling by SecM at multiple elongation steps

Zhang, J.Pan, X.Yan, K.Sun, S.Gao, N.Sui, S.F.

(2015) Elife 4

  • DOI: 10.7554/eLife.09684
  • Primary Citation of Related Structures:  
    3JBU, 3JBV

  • PubMed Abstract: 
  • Regulation of translating ribosomes is a major component of gene expression control network. In Escherichia coli, ribosome stalling by the C-terminal arrest sequence of SecM regulates the SecA-dependent secretion pathway. Previous studies reported many residues of SecM peptide and ribosome exit tunnel are critical for stalling ...

    Regulation of translating ribosomes is a major component of gene expression control network. In Escherichia coli, ribosome stalling by the C-terminal arrest sequence of SecM regulates the SecA-dependent secretion pathway. Previous studies reported many residues of SecM peptide and ribosome exit tunnel are critical for stalling. However, the underlying molecular mechanism is still not clear at the atomic level. Here, we present two cryo-EM structures of the SecM-stalled ribosomes at 3.3-3.7 Å resolution, which reveal two different stalling mechanisms at distinct elongation steps of the translation cycle: one is due to the inactivation of ribosomal peptidyl-transferase center which inhibits peptide bond formation with the incoming prolyl-tRNA; the other is the prolonged residence of the peptidyl-RNA at the hybrid A/P site which inhibits the full-scale tRNA translocation. These results demonstrate an elegant control of translation cycle by regulatory peptides through a continuous, dynamic reshaping of the functional center of the ribosome.


    Organizational Affiliation

    State Key Laboratory of Membrane Biology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.



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30S ribosomal protein S2B241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3C233Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S4D206Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S5E167Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S6F131Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S7G156Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S10J103Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11K129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S20T87Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S21U71Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L28Y [auth 0]78Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L29Z [auth 1]63Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L30AA [auth 2]59Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L32BA [auth 3]57Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L33CA [auth 4]55Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L34DA [auth 6]46Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L35EA [auth 7]65Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L36FA [auth 8]38Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L2IA [auth c]273Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L9JA [auth i]142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L11KA [auth d]209Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L3LA [auth e]201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L4MA [auth f]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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50S ribosomal protein L5NA [auth g]177Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6OA [auth h]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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50S ribosomal protein L13PA [auth j]142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14QA [auth k]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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50S ribosomal protein L15RA [auth l]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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50S ribosomal protein L16SA [auth m]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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50S ribosomal protein L17TA [auth n]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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50S ribosomal protein L18UA [auth o]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19VA [auth p]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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50S ribosomal protein L20WA [auth q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21XA [auth r]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22YA [auth s]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23ZA [auth t]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24AB [auth u]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25BB [auth w]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L27CB [auth y]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Secretion monitorDB [auth z]27Escherichia coli K-12Mutation(s): 0 
Gene Names: secMsrrAyacAb0097JW5007
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RNA (1530-MER)A1542Escherichia coli K-12
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RNA (76-MER)V76Escherichia coli K-12
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RNA (75-MER)W75Escherichia coli K-12
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    RNA (5'-R(P*CP*UP*GP*GP*CP*CP*CP*UP*CP*AP*A)-3')X11Escherichia coli K-12
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    RNA (118-MER)GA [auth a]120Escherichia coli K-12
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    RNA (2903-MER)HA [auth b]2904Escherichia coli K-12
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    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    CLM (Subject of Investigation/LOI)
    Query on CLM

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    EB [auth b]CHLORAMPHENICOL
    C11 H12 Cl2 N2 O5
    WIIZWVCIJKGZOK-RKDXNWHRSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.32 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: 2016-01-27
      Type: Initial release
    • Version 1.1: 2017-02-08
      Changes: Database references
    • Version 1.2: 2018-06-06
      Changes: Data collection, Database references, Other, Source and taxonomy, Structure summary
    • Version 1.3: 2018-07-18
      Changes: Data collection, Database references
    • Version 1.4: 2019-12-18
      Changes: Data collection