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Yorodumi- PDB-7kwg: Staphylococcus aureus 30S ribosomal subunit in presence of spermidine -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kwg | |||||||||
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Title | Staphylococcus aureus 30S ribosomal subunit in presence of spermidine | |||||||||
Components |
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Keywords | RIBOSOME / Pathogen / small ribosomal subunit / spermidine | |||||||||
Function / homology | Function and homology information 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 ...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) Staphylococcus aureus (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 Å | |||||||||
Authors | Belinite, M. / Khusainov, I. / Marzi, S. / Romby, P. / Yusupov, M. / Hashem, Y. | |||||||||
Funding support | France, 2items
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Citation | Journal: Front Mol Biosci / Year: 2021 Title: Stabilization of Ribosomal RNA of the Small Subunit by Spermidine in . Authors: Margarita Belinite / Iskander Khusainov / Heddy Soufari / Stefano Marzi / Pascale Romby / Marat Yusupov / Yaser Hashem / Abstract: Cryo-electron microscopy is now used as a method of choice in structural biology for studying protein synthesis, a process mediated by the ribosome machinery. In order to achieve high-resolution ...Cryo-electron microscopy is now used as a method of choice in structural biology for studying protein synthesis, a process mediated by the ribosome machinery. In order to achieve high-resolution structures using this approach, one needs to obtain homogeneous and stable samples, which requires optimization of ribosome purification in a species-dependent manner. This is especially critical for the bacterial small ribosomal subunit that tends to be unstable in the absence of ligands. Here, we report a protocol for purification of stable 30 S from the Gram-positive bacterium and its cryo-EM structures: in presence of spermidine at a resolution ranging between 3.4 and 3.6 Å and in its absence at 5.3 Å. Using biochemical characterization and cryo-EM, we demonstrate the importance of spermidine for stabilization of the 30 S preserving favorable conformation of the helix 44. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7kwg.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7kwg.ent.gz | 899.7 KB | Display | PDB format |
PDBx/mmJSON format | 7kwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kwg_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7kwg_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7kwg_validation.xml.gz | 98.6 KB | Display | |
Data in CIF | 7kwg_validation.cif.gz | 164.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/7kwg ftp://data.pdbj.org/pub/pdb/validation_reports/kw/7kwg | HTTPS FTP |
-Related structure data
Related structure data | 23052MC 7bgdC 7bgeC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules Aa
#1: RNA chain | Mass: 10392.300 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) Strain: NCTC 8325 / PS 47 / Production host: Escherichia coli (E. coli) |
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#2: RNA chain | Mass: 503218.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria) References: GenBank: 87201381 |
-30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst
#3: Protein | Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FZ25 |
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#4: Protein | Mass: 24143.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW12 |
#5: Protein | Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FXK6 |
#6: Protein | Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW23 |
#7: Protein | Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2G113 |
#8: Protein | Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: P48940 |
#9: Protein | Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW20 |
#10: Protein | Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW39 |
#11: Protein | Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: A0A380EDM5, UniProt: Q931G5*PLUS |
#12: Protein | Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW31 |
#13: Protein | Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: P0A0H0 |
#14: Protein | Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW30 |
#15: Protein | Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW19 |
#16: Protein | Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2G2Q1 |
#17: Protein | Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FZ45 |
#18: Protein | Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW15 |
#19: Protein | Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2G111 |
#20: Protein | Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FW10 |
#21: Protein | Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) Strain: NCTC 8325 / PS 47 / References: UniProt: Q2FXY6 |
-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 | Name: Staphylococcus aureus 30S ribosomal subunit in presence of spermidine Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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: OTHER |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 3 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: Gctf / Version: 1.06 / Category: CTF correction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 529602 / Symmetry type: POINT |