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- PDB-7bgd: 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: 7bgd | |||||||||
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Title | Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (body only) | |||||||||
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![]() | RIBOSOME / Pathogen / small ribosomal subunit / spermidine | |||||||||
Function / homology | ![]() ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex ...ribosomal small subunit biogenesis / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 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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Download
PDBx/mmCIF format | ![]() | 816.7 KB | Display | ![]() |
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PDB format | ![]() | 614.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 853.2 KB | Display | ![]() |
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Full document | ![]() | 977.3 KB | Display | |
Data in XML | ![]() | 64.1 KB | Display | |
Data in CIF | ![]() | 109.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12178MC ![]() 7bgeC ![]() 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 , 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.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 503218.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-30S ribosomal protein ... , 12 types, 12 molecules bdefhklopqrt
#3: 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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#4: Protein | Mass: 23051.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FXK6 |
#5: Protein | Mass: 17770.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW23 |
#6: Protein | Mass: 11613.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2G113 |
#7: Protein | Mass: 14854.315 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW20 |
#8: Protein | Mass: 13907.978 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW31 |
#9: Protein | Mass: 15320.870 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: P0A0H0 |
#10: Protein | Mass: 10634.330 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2G2Q1 |
#11: Protein | Mass: 10253.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FZ45 |
#12: Protein | Mass: 10196.888 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2FW15 |
#13: Protein | Mass: 9332.018 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / References: UniProt: Q2G111 |
#14: Protein | Mass: 9039.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() Strain: NCTC 8325 / 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 |
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Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||||||
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 |
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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 | Name: Gctf / Version: 1.06 / Category: CTF correction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 529602 / Symmetry type: POINT |