5NJT

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization.

Beckert, B.Abdelshahid, M.Schafer, H.Steinchen, W.Arenz, S.Berninghausen, O.Beckmann, R.Bange, G.Turgay, K.Wilson, D.N.

(2017) EMBO J 36: 2061-2072

  • DOI: https://doi.org/10.15252/embj.201696189
  • Primary Citation of Related Structures:  
    5NJT

  • PubMed Abstract: 

    Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In Escherichia coli , dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of E. coli 100S ( Ec 100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the Bacillus subtilis hibernating 100S ( Bs 100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the Bs HPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as E. coli .


  • Organizational Affiliation

    Gene Center, Department for Biochemistry and Center for integrated Protein Science Munich (CiPSM), University of Munich, Munich, Germany.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2224Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3210Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4199Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5165Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S695Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7153Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9130Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11118Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12137Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13111Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1460Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1588Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1689Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1786Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1871Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1980Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2086Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2275Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4205Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5178Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6AA [auth a]175Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10BA [auth b]123Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13CA [auth c]142Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14DA [auth d]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15EA [auth e]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16FA [auth f]138Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17GA [auth g]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18HA [auth h]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19IA [auth i]114Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20JA [auth j]117Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21KA [auth k]101Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22LA [auth l]109Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23MA [auth m]93Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24NA [auth n]100Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27OA [auth o]82Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32PA [auth p]54Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 1QA [auth q]48Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34RA [auth r]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35SA [auth s]64Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36TA [auth t]36Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth u]58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth v]65Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30WA [auth w]58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P19947 (Bacillus subtilis (strain 168))
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Go to UniProtKB:  P19947
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UniProt GroupP19947
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31XA [auth y]64Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for Q03223 (Bacillus subtilis (strain 168))
Explore Q03223 
Go to UniProtKB:  Q03223
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UniProt GroupQ03223
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome hibernation promotion factorYA [auth x]104Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
UniProt
Find proteins for P28368 (Bacillus subtilis (strain 168))
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Go to UniProtKB:  P28368
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UniProt GroupP28368
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,544Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 21
MoleculeChains LengthOrganismImage
23S ribosomal RNA2,923Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 22
MoleculeChains LengthOrganismImage
5S ribosomal RNA112Bacillus subtilis subsp. subtilis str. 168
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONFREALIGN9.11

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP-1879

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-07-05
    Changes: Structure summary
  • Version 1.2: 2017-07-26
    Changes: Database references
  • Version 1.3: 2017-08-02
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations