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 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/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. 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.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2241Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
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30S ribosomal protein S3233Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6131Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
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30S ribosomal protein S7156Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8130Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S9130Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S10103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S11129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14101Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
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30S ribosomal protein S1589Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1682Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S1784Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1875Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1992Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2087Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2171Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Y [auth 0]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29Z [auth 1]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30AA [auth 2]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BA [auth 3]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CA [auth 4]55Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34DA [auth 6]46Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35EA [auth 7]65Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36FA [auth 8]38Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2IA [auth c]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11JA [auth i]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3KA [auth d]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4LA [auth e]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5MA [auth f]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L6NA [auth g]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9OA [auth h]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
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50S ribosomal protein L13PA [auth j]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14QA [auth k]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15RA [auth l]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
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50S ribosomal protein L16SA [auth m]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17TA [auth n]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18UA [auth o]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19VA [auth p]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20WA [auth q]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21XA [auth r]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22YA [auth s]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23ZA [auth t]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24AB [auth u]104Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P60624 (Escherichia coli (strain K12))
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UniProt GroupP60624
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25BB [auth w]94Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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UniProt GroupP68919
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27CB [auth y]85Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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UniProt GroupP0A7L8
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Secretion monitorDB [auth z]27Escherichia coli K-12Mutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (1530-MER)1,542Escherichia coli K-12
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Entity ID: 22
MoleculeChains LengthOrganismImage
RNA (76-MER)76Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
RNA (75-MER)75Escherichia coli K-12
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Entity ID: 24
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*UP*GP*GP*CP*CP*CP*UP*CP*AP*A)-3')11Escherichia coli K-12
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Entity ID: 33
MoleculeChains LengthOrganismImage
RNA (118-MER)GA [auth a]120Escherichia coli K-12
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Entity ID: 34
MoleculeChains LengthOrganismImage
RNA (2903-MER)HA [auth b]2,904Escherichia coli K-12
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLM
Query on CLM

Download Ideal Coordinates CCD File 
EB [auth b]CHLORAMPHENICOL
C11 H12 Cl2 N2 O5
WIIZWVCIJKGZOK-RKDXNWHRSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.32 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

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
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary