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- PDB-8e33: E. coli 50S ribosome bound to compound streptogramin analog SAB001 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8.0E+33 | ||||||||||||
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Title | E. coli 50S ribosome bound to compound streptogramin analog SAB001 | ||||||||||||
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![]() | RIBOSOME/ANTIBIOTIC / E. coli ribosome / streptogramin A / streptogramin B / antibiotics / RIBOSOME-ANTIBIOTIC complex | ||||||||||||
Function / homology | ![]() DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / cytosolic large ribosomal subunit ...DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit assembly / large ribosomal subunit / large ribosomal subunit rRNA binding / transferase activity / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / response to antibiotic / RNA binding / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.23 Å | ||||||||||||
![]() | Pellegrino, J. / Lee, D.J. / Fraser, J.S. / Seiple, I.B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Potential for clicked streptogramin analogs Authors: Takahashi, Y. / Pellegrino, J. / Lee, D.J. / Fraser, J.S. / Seiple, I.B. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 91.4 KB | Display | |
Data in CIF | ![]() | 155.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27855MC ![]() 8e30C ![]() 8e32C ![]() 8e35C ![]() 8e36C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-RNA chain , 2 types, 2 molecules IJ
#1: RNA chain | Mass: 941795.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: RNA chain | Mass: 38177.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-50S ribosomal protein ... , 8 types, 8 molecules KLMNOPQR
#3: Protein | Mass: 29663.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#4: Protein | Mass: 15008.471 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#5: Protein | Mass: 22121.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#6: Protein | Mass: 22277.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#7: Protein | Mass: 16050.606 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#8: Protein | Mass: 12253.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#9: Protein | Mass: 6332.249 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#10: Protein/peptide | Mass: 5397.463 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/UDU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#11: Chemical | ChemComp-UDU / |
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#12: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-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: 50S E. coli ribosome / Type: RIBOSOME / Entity ID: #1-#10 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | 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: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162125 / Symmetry type: POINT |