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 

wwPDB Validation   3D Report Full Report


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: 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) ...

    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

    Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2B224Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsBBSU16490
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Entity ID: 3
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30S ribosomal protein S3C210Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsCBSU01220
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Entity ID: 4
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30S ribosomal protein S4D199Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsDBSU29660
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5E165Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsEspcABSU01330
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Entity ID: 6
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30S ribosomal protein S6F95Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsFBSU40910
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Entity ID: 7
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30S ribosomal protein S7G153Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsGBSU01110
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Entity ID: 8
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30S ribosomal protein S8H131Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsHBSU01300
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Entity ID: 9
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30S ribosomal protein S9I130Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsIBSU01500
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Entity ID: 10
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30S ribosomal protein S10J102Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsJtetABSU01150
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Entity ID: 11
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30S ribosomal protein S11K118Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsKBSU01420
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Entity ID: 12
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30S ribosomal protein S12L137Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsLfunstrABSU01100
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Entity ID: 13
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30S ribosomal protein S13M111Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsMBSU01410
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Entity ID: 14
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30S ribosomal protein S14N60Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsN1rpsNrpsNArpsZBSU01290
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Entity ID: 15
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30S ribosomal protein S15O88Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsOBSU16680
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Entity ID: 16
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30S ribosomal protein S16P89Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsPBSU15990
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Entity ID: 17
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30S ribosomal protein S17Q86Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsQBSU01250
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Entity ID: 18
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30S ribosomal protein S18R71Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsRBSU40890
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Entity ID: 19
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30S ribosomal protein S19S80Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsSBSU01200
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Entity ID: 20
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30S ribosomal protein S20T86Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpsTyqeOBSU25550
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Entity ID: 23
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50S ribosomal protein L2W275Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplBBSU01190
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Entity ID: 24
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50S ribosomal protein L3X207Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplCBSU01160
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Entity ID: 25
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50S ribosomal protein L4Y205Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplDBSU01170
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Entity ID: 26
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50S ribosomal protein L5Z178Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplEBSU01280
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Entity ID: 27
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50S ribosomal protein L6AA [auth a]175Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplFBSU01310
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50S ribosomal protein L10BA [auth b]123Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplJBSU01040
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50S ribosomal protein L13CA [auth c]142Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplMBSU01490
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50S ribosomal protein L14DA [auth d]122Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplNBSU01260
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Entity ID: 31
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50S ribosomal protein L15EA [auth e]146Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplOBSU01350
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50S ribosomal protein L16FA [auth f]138Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplPBSU01230
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Entity ID: 33
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50S ribosomal protein L17GA [auth g]119Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplQBSU01440
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Entity ID: 34
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50S ribosomal protein L18HA [auth h]120Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplRBSU01320
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50S ribosomal protein L19IA [auth i]114Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplSBSU16040
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50S ribosomal protein L20JA [auth j]117Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplTBSU28850
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50S ribosomal protein L21KA [auth k]101Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplUBSU27960
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50S ribosomal protein L22LA [auth l]109Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplVBSU01210
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50S ribosomal protein L23MA [auth m]93Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplWBSU01180
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50S ribosomal protein L24NA [auth n]100Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rplXBSU01270
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50S ribosomal protein L27OA [auth o]82Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmABSU27940
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50S ribosomal protein L32PA [auth p]54Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmFBSU15080
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50S ribosomal protein L33 1QA [auth q]48Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmGArpmG1BSU24900
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50S ribosomal protein L34RA [auth r]44Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmHBSU41060
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50S ribosomal protein L35SA [auth s]64Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmIBSU28860
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36TA [auth t]36Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmJBSU01400
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Find proteins for P20278 (Bacillus subtilis (strain 168))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth u]58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmByloTBSU15820
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Find proteins for P37807 (Bacillus subtilis (strain 168))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth v]65Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmCBSU01240
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Find proteins for P12873 (Bacillus subtilis (strain 168))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30WA [auth w]58Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmDBSU01340
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Find proteins for P19947 (Bacillus subtilis (strain 168))
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UniProt GroupP19947
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31XA [auth y]64Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: rpmEBSU37070
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Find proteins for Q03223 (Bacillus subtilis (strain 168))
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UniProt GroupQ03223
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosome hibernation promotion factorYA [auth x]104Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yvyDhpfyviIBSU35310orf189
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Find proteins for P28368 (Bacillus subtilis (strain 168))
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Entity ID: 1
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16S ribosomal RNAA 1544Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 21
MoleculeChainsLengthOrganismImage
23S ribosomal RNAU 2923Bacillus subtilis subsp. subtilis str. 168
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Entity ID: 22
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5S ribosomal RNAV 112Bacillus 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 

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