8BYV | pdb_00008byv

Cryo-EM structure of a Staphylococus aureus 30S-RbfA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from S. aureus.

Bikmullin, A.G.Fatkhullin, B.Stetsenko, A.Gabdulkhakov, A.Garaeva, N.Nurullina, L.Klochkova, E.Golubev, A.Khusainov, I.Trachtmann, N.Blokhin, D.Guskov, A.Validov, S.Usachev, K.Yusupov, M.

(2023) Int J Mol Sci 24

  • DOI: https://doi.org/10.3390/ijms24032118
  • Primary Citation of Related Structures:  
    8BXA, 8BYV

  • PubMed Abstract: 

    Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins' folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S-RbfA complex from Staphylococcus aureus ( S. aureus ). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that S. aureus is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens.


  • Organizational Affiliation
    • Laboratory of Structural Biology, Institute of Fundamental Medicine and Biology, Kazan Federal University, 420021 Kazan, Russia.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth b]255Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FZ25 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth c]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW12 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth d]200Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth e]166Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW23 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth f]98Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth g]156Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth h]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth i]132Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth j]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q931G5 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth k]129Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW31 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth l]137Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for P0A0H0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth m]121Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW30 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth n]61Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth o]89Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2G2Q1 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth p]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth q]87Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth r]80Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth s]92Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FW10 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth t]83Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
Find proteins for Q2FXY6 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosome-binding factor AU [auth A]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rbfASAOUHSC_01247
UniProt
Find proteins for Q2G2Q4 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth a]1,547Staphylococcus aureus subsp. aureus NCTC 8325
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Foundation for Basic ResearchRussian Federation20-54-15001

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Data collection, Database references