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:  
    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: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0],
EB [auth 00]
56Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 2
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50S ribosomal protein L33B [auth 1],
FB [auth 11]
50Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 3
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50S ribosomal protein L34C [auth 2],
GB [auth 22]
46Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 4
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50S ribosomal protein L35D [auth 3],
HB [auth 33]
64Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 5
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50S ribosomal protein L36E [auth 4],
IB [auth 44]
38Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L31F [auth 6],
JB [auth 66]
66Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L2I [auth C],
MB [auth CC]
271Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L3J [auth D],
NB [auth DD]
209Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L4K [auth E],
OB [auth EE]
201Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L5L [auth F],
PB [auth FF]
177Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L6M [auth G],
QB [auth GG]
176Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L9N [auth H],
RB [auth HH]
149Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L13O [auth J],
SB [auth JJ]
142Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L14P [auth K],
TB [auth KK]
122Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L15Q [auth L],
UB [auth LL]
143Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L16R [auth M],
VB [auth MM]
136Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L17S [auth N],
WB [auth NN]
120Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L18T [auth O],
XB [auth OO]
116Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L19U [auth P],
YB [auth PP]
114Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L20V [auth Q],
ZB [auth QQ]
117Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L21W [auth R],
AC [auth RR]
103Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L22X [auth S],
BC [auth SS]
110Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L23Y [auth T],
CC [auth TT]
93Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L24Z [auth U],
DC [auth UU]
102Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L25AA [auth V],
EC [auth VV]
94Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L27BA [auth W],
FC [auth WW]
75Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L28CA [auth X],
GC [auth XX]
77Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L29DA [auth Y],
HC [auth YY]
63Escherichia coli BW25113Mutation(s): 0 
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50S ribosomal protein L30EA [auth Z],
IC [auth ZZ]
58Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 33
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30S ribosomal protein S2GA [auth b],
KC [auth bb]
226Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 34
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30S ribosomal protein S3HA [auth c],
LC [auth cc]
206Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S4IA [auth d],
MC [auth dd]
205Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S5JA [auth e],
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157Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S6KA [auth f],
OC [auth ff]
100Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S7LA [auth g],
PC [auth gg]
161Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S8MA [auth h],
QC [auth hh]
129Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S9NA [auth i],
RC [auth ii]
127Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S10OA [auth j],
SC [auth jj]
98Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S11PA [auth k],
TC [auth kk]
116Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S12QA [auth l],
UC [auth ll]
123Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S13RA [auth m],
VC [auth mm]
114Escherichia coli BW25113Mutation(s): 0 
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30S ribosomal protein S14SA [auth n],
WC [auth nn]
101Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth o],
XC [auth oo]
88Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth p],
YC [auth pp]
82Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth q],
ZC [auth qq]
80Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth r],
AD [auth rr]
65Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth s],
BD [auth ss]
79Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20YA [auth t],
CD [auth tt]
85Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21ZA [auth u],
DD [auth uu]
65Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome modulation factorAB [auth v],
ED [auth vv]
55Escherichia coli BW25113Mutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promoting factorBB [auth x],
FD [auth xx]
95Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S1CB [auth y],
GD [auth yy]
557Escherichia coli BW25113Mutation(s): 0 
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Entity ID: 7
MoleculeChainsLengthOrganismImage
23S ribosomal RNAG [auth A],
KB [auth AA]
2,903Escherichia coli BW25113
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Entity ID: 8
MoleculeChainsLengthOrganismImage
5S ribosomal RNAH [auth B],
LB [auth BB]
120Escherichia coli BW25113
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Entity ID: 32
MoleculeChainsLengthOrganismImage
16S ribosomal RNAFA [auth a],
JC [auth aa]
1,539Escherichia coli BW25113
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Entity ID: 56
MoleculeChainsLengthOrganismImage
tRNA MixtureDB [auth w],
HD [auth ww]
77Escherichia coli BW25113
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 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