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- PDB-7bge: Staphylococcus aureus 30S ribosomal subunit in presence of spermi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bge | |||||||||
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Title | Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head only) | |||||||||
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![]() | RIBOSOME / Pathogen / small ribosomal subunit / spermidine | |||||||||
Function / homology | ![]() ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / RNA binding ...ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / mRNA binding / RNA binding / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Belinite, M. / Khusainov, I. / Marzi, S. / Romby, P. / Yusupov, M. / Hashem, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 416.4 KB | Display | ![]() |
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PDB format | ![]() | 302.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12179MC ![]() 7bgdC ![]() 7kwgC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 1 types, 1 molecules a
#1: RNA chain | Mass: 503218.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() |
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-30S ribosomal protein ... , 8 types, 8 molecules bcgijmns
#2: Protein | Mass: 29136.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / 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) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW12 |
#4: Protein | Mass: 17826.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: P48940 |
#5: Protein | Mass: 14856.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW39 |
#6: Protein | Mass: 11600.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q931G5 |
#7: Protein | Mass: 13747.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW30 |
#8: Protein | Mass: 7317.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW19 |
#9: Protein | Mass: 10639.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW10 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head only) Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 3 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 529602 / Symmetry type: POINT |