6H58

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 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:  
    6H58, 6H4N

  • 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 fac ...

    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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50S ribosomal protein L3200056Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3DDD209Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L4EEE201Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L5FFF177Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L6GGG176Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L9HHH149Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L13JJJ142Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L14KKK122Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L15LLL143Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L16MMM136Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L17NNN120Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3311150Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L18OOO116Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L19PPP114Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L20QQQ117Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L21RRR103Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L22SSS110Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L23TTT93Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L24UUU102Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L25VVV94Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L27WWW75Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L28XXX77Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3422246Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L29YYY63Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L30ZZZ58Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S2bbb226Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S3ccc206Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S4ddd205Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S5eee157Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S6fff100Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S7ggg161Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S8hhh129Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3533364Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S9iii127Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S10jjj98Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S11kkk116Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S12lll123Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S13mmm114Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S14nnn101Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S15ooo88Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S16ppp82Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S17qqq80Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S18rrr65Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3644438Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S19sss79Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S20ttt85Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S21uuu65Escherichia coli BW25113Mutation(s): 0 
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Ribosome modulation factorvvv55Escherichia coli BW25113Mutation(s): 0 
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Ribosome hibernation promoting factorxxx95Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S1yyy557Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3166666Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L2CCC271Escherichia coli BW25113Mutation(s): 0 
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16S ribosomal RNAa, aa1539Escherichia coli BW25113
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tRNA Mixturew, ww77Escherichia coli BW25113
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23S ribosomal RNAA, AA2903Escherichia coli BW25113
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5S ribosomal RNAB, BB120Escherichia coli BW25113
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GermanySPP1879
GermanyFOR1805

Revision History 

  • 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