6H4N

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1 - 70S Hibernating E. coli Ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1.

Beckert, B.Turk, M.Czech, A.Berninghausen, O.Beckmann, R.Ignatova, Z.Plitzko, J.M.Wilson, D.N.

(2018) Nat Microbiol 3: 1115-1121

  • DOI: 10.1038/s41564-018-0237-0
  • Primary Citation of Related Structures:  
    6H4N, 6H58

  • PubMed Abstract: 
  • To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles 1 . In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF) 2-4 ...

    To survive under conditions of stress, such as nutrient deprivation, bacterial 70S ribosomes dimerize to form hibernating 100S particles 1 . In γ-proteobacteria, such as Escherichia coli, 100S formation requires the ribosome modulation factor (RMF) and the hibernation promoting factor (HPF) 2-4 . Here we present single-particle cryo-electron microscopy structures of hibernating 70S and 100S particles isolated from stationary-phase E. coli cells at 3.0 Å and 7.9 Å resolution, respectively. The structures reveal the binding sites for HPF and RMF as well as the unexpected presence of deacylated E-site transfer RNA and ribosomal protein bS1. HPF interacts with the anticodon-stem-loop of the E-tRNA and occludes the binding site for the messenger RNA as well as A- and P-site tRNAs. RMF facilitates stabilization of a compact conformation of bS1, which together sequester the anti-Shine-Dalgarno sequence of the 16S ribosomal RNA (rRNA), thereby inhibiting translation initiation. At the dimerization interface, the C-terminus of uS2 probes the mRNA entrance channel of the symmetry-related particle, thus suggesting that dimerization inactivates ribosomes by blocking the binding of mRNA within the channel. The back-to-back E. coli 100S arrangement is distinct from 100S particles observed previously in Gram-positive bacteria 5-8 , and reveals a unique role for bS1 in translation regulation.


    Organizational Affiliation

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany. Daniel.wilson@chemie.uni-hamburg.de.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]218Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S3C [auth c]206Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 4
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30S ribosomal protein S4D [auth d]205Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 5
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30S ribosomal protein S5E [auth e]157Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 6
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30S ribosomal protein S6F [auth f]100Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S7G [auth g]161Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S8H [auth h]129Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S9I [auth i]127Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S10J [auth j]98Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S11K [auth k]116Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S12L [auth l]123Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S13M [auth m]114Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S14N [auth n]101Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S15O [auth o]88Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S16P [auth p]82Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S17Q [auth q]80Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S18R [auth r]65Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S19S [auth s]79Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S20T [auth t]85Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S21U [auth u]65Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L2X [auth C]271Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3Y [auth D]209Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L4Z [auth E]201Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L5AA [auth F]177Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L6BA [auth G]176Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L9CA [auth H]149Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L13DA [auth J]142Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L14EA [auth K]122Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L15FA [auth L]143Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L16GA [auth M]136Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L17HA [auth N]120Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L18IA [auth O]116Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L19JA [auth P]114Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L20KA [auth Q]117Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L21LA [auth R]103Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L22MA [auth S]110Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L23NA [auth T]93Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L24OA [auth U]102Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L25PA [auth V]94Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L27QA [auth W]75Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L28RA [auth X]77Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L29SA [auth Y]63Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L30TA [auth Z]58Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L32UA [auth 0]56Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L33VA [auth 1]50Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L34WA [auth 2]46Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L35XA [auth 3]64Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L36YA [auth 4]38Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L31ZA [auth 6]66Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 54
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Ribosome modulation factorBB [auth v]55Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S1CB [auth y]557Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 56
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Ribosome hibernation promoting factorDB [auth x]95Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 1
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16S ribosomal RNAA [auth a]1534Escherichia coli BW25113
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Entity ID: 22
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23S ribosomal RNAV [auth A]2903Escherichia coli BW25113
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Entity ID: 23
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5S ribosomal RNAW [auth B]120Escherichia coli BW25113
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Entity ID: 53
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tRNAAB [auth w]77Escherichia coli BW25113
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  • Entity ID: 57
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    RNA (5'-R(P*CP*UP*CP*CP*U)-3')EB [auth I]5Escherichia coli BW25113
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    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.00 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    GermanySPP1879
    GermanyFOR1805

    Revision History  (Full details and data files)

    • Version 1.0: 2018-09-05
      Type: Initial release
    • Version 1.1: 2018-09-12
      Changes: Data collection, Database references
    • Version 1.2: 2018-10-03
      Changes: Data collection, Database references
    • Version 1.3: 2018-10-24
      Changes: Advisory, Data collection, Derived calculations