6SZS

Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Release factor-dependent ribosome rescue by BrfA in the Gram-positive bacterium Bacillus subtilis.

Shimokawa-Chiba, N.Muller, C.Fujiwara, K.Beckert, B.Ito, K.Wilson, D.N.Chiba, S.

(2019) Nat Commun 10: 5397-5397

  • DOI: https://doi.org/10.1038/s41467-019-13408-7
  • Primary Citation of Related Structures:  
    6SZS

  • PubMed Abstract: 

    Rescue of the ribosomes from dead-end translation complexes, such as those on truncated (non-stop) mRNA, is essential for the cell. Whereas bacteria use trans-translation for ribosome rescue, some Gram-negative species possess alternative and release factor (RF)-dependent rescue factors, which enable an RF to catalyze stop-codon-independent polypeptide release. We now discover that the Gram-positive Bacillus subtilis has an evolutionarily distinct ribosome rescue factor named BrfA. Genetic analysis shows that B. subtilis requires the function of either trans-translation or BrfA for growth, even in the absence of proteotoxic stresses. Biochemical and cryo-electron microscopy (cryo-EM) characterization demonstrates that BrfA binds to non-stop stalled ribosomes, recruits homologous RF2, but not RF1, and induces its transition into an open active conformation. Although BrfA is distinct from E. coli ArfA, they use convergent strategies in terms of mode of action and expression regulation, indicating that many bacteria may have evolved as yet unidentified ribosome rescue systems.


  • Organizational Affiliation

    Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 2
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50S ribosomal protein L33B [auth 1]55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]65Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31F [auth 5]70Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmEb3936JW3907
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth C]273Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3J [auth D]209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L4K [auth E]201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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50S ribosomal protein L5L [auth F]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 13
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50S ribosomal protein L6M [auth G]177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 14
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50S ribosomal protein L9N [auth H]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 15
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50S ribosomal protein L13O [auth J]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 16
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50S ribosomal protein L14P [auth K]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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50S ribosomal protein L15Q [auth L]144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 18
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50S ribosomal protein L16R [auth M]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 19
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50S ribosomal protein L17S [auth N]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 20
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50S ribosomal protein L18T [auth O]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 21
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50S ribosomal protein L19U [auth P]115Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 22
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50S ribosomal protein L20V [auth Q]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 23
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50S ribosomal protein L21W [auth R]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 24
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50S ribosomal protein L22X [auth S]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 25
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50S ribosomal protein L23Y [auth T]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24Z [auth U]104Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 27
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50S ribosomal protein L25AA [auth V]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 28
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50S ribosomal protein L27BA [auth W]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28CA [auth X]78Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29DA [auth Y]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30EA [auth Z]59Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 33
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30S ribosomal protein S2GA [auth b]241Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 34
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30S ribosomal protein S3HA [auth c]233Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 35
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30S ribosomal protein S4IA [auth d]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 36
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30S ribosomal protein S5JA [auth e]167Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 37
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30S ribosomal protein S6KA [auth f]135Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7LA [auth g]179Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 39
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30S ribosomal protein S8MA [auth h]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9NA [auth i]130Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 41
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30S ribosomal protein S10OA [auth j]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 42
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30S ribosomal protein S11PA [auth k]129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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30S ribosomal protein S12QA [auth l]124Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13RA [auth m]118Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14SA [auth n]101Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15TA [auth o]89Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16UA [auth p]82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17VA [auth q]84Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18WA [auth r]75Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19XA [auth s]92Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
UniProt
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20YA [auth t]87Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21ZA [auth u]71Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein YqkKCB [auth y]71Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yqkKBSU23540
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide chain release factor 2DB [auth z]362Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: prfBBSU35290
UniProt
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Entity ID: 7
MoleculeChains LengthOrganismImage
23S ribosomal RNAG [auth A]2,903Escherichia coli K-12
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Entity ID: 8
MoleculeChains LengthOrganismImage
5S ribosomal RNAH [auth B]120Escherichia coli K-12
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Entity ID: 32
MoleculeChains LengthOrganismImage
16S ribosomal RNAFA [auth a]1,540Escherichia coli K-12
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth v]6Escherichia coli K-12
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Entity ID: 54
MoleculeChains LengthOrganismImage
P-site tRNA-Pro(CGG)BB [auth x]77Escherichia coli K-12
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.06 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySPP1879-WI3285/5-2

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2024-05-22
    Changes: Data collection, Database references, Refinement description