+Open data
-Basic information
Entry | Database: PDB / ID: 8byv | ||||||
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Title | Cryo-EM structure of a Staphylococus aureus 30S-RbfA complex | ||||||
Components |
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Keywords | RIBOSOME / RbfA / 30S subunit maturation / cryo-EM / ribosome biogenesis / translation / Staphylococcus aureus | ||||||
Function / homology | Function and homology information ribosomal small subunit binding / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding ...ribosomal small subunit binding / maturation of SSU-rRNA / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||
Authors | Bikmullin, A.G. / Fatkhullin, B. / Stetsenko, A. / Guskov, A. / Yusupov, M. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from . Authors: Aydar G Bikmullin / Bulat Fatkhullin / Artem Stetsenko / Azat Gabdulkhakov / Natalia Garaeva / Liliia Nurullina / Evelina Klochkova / Alexander Golubev / Iskander Khusainov / Natalie ...Authors: Aydar G Bikmullin / Bulat Fatkhullin / Artem Stetsenko / Azat Gabdulkhakov / Natalia Garaeva / Liliia Nurullina / Evelina Klochkova / Alexander Golubev / Iskander Khusainov / Natalie Trachtmann / Dmitriy Blokhin / Albert Guskov / Shamil Validov / Konstantin Usachev / Marat Yusupov / 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 ...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 (). 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 is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8byv.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8byv.ent.gz | 1016.8 KB | Display | PDB format |
PDBx/mmJSON format | 8byv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/8byv ftp://data.pdbj.org/pub/pdb/validation_reports/by/8byv | HTTPS FTP |
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-Related structure data
Related structure data | 16334MC 8bxaC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst
#2: Protein | Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FZ25 |
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#3: Protein | Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW12 |
#4: Protein | Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FXK6 |
#5: Protein | Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW23 |
#6: Protein | Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2G113 |
#7: Protein | Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: P48940 |
#8: Protein | Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW20 |
#9: Protein | Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW39 |
#10: Protein | Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q931G5 |
#11: Protein | Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW31 |
#12: Protein | Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: P0A0H0 |
#13: Protein | Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW30 |
#14: Protein | Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW19 |
#15: Protein | Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2G2Q1 |
#16: Protein | Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FZ45 |
#17: Protein | Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW15 |
#18: Protein | Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2G111 |
#19: Protein | Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FW10 |
#20: Protein | Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: UniProt: Q2FXY6 |
-RNA chain / Protein , 2 types, 2 molecules aA
#1: RNA chain | Mass: 500464.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: 87201381 |
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#21: Protein | Mass: 13535.722 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Gene: rbfA, SAOUHSC_01247 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G2Q4 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 53.3 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software |
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EM software | Name: EPU / Category: image acquisition | |||||||||
CTF correction | Type: NONE | |||||||||
3D reconstruction | Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81421 / Symmetry type: POINT | |||||||||
Refinement | Cross valid method: NONE |