+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27857 | |||||||||
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Title | E. coli 50S ribosome bound to compound SAB002 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | E. coli ribosome / streptogramin A / streptogramin B / antibiotics / RIBOSOME-ANTIBIOTIC complex | |||||||||
Function / homology | Function and homology information DnaA-L2 complex / negative regulation of DNA-templated DNA replication initiation / ribosome assembly / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / large ribosomal subunit / ribosomal large subunit assembly / 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 / large ribosomal subunit / ribosomal large subunit assembly / 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 | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.27 Å | |||||||||
Authors | Pellegrino J / Lee DJ / Fraser JS / Seiple IB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Potential for clicked streptogramin analogs Authors: Takahashi Y / Pellegrino J / Lee DJ / Fraser JS / Seiple IB | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27857.map.gz | 474.1 MB | EMDB map data format | |
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Header (meta data) | emd-27857-v30.xml emd-27857.xml | 27.3 KB 27.3 KB | Display Display | EMDB header |
Images | emd_27857.png | 176.2 KB | ||
Filedesc metadata | emd-27857.cif.gz | 8.2 KB | ||
Others | emd_27857_half_map_1.map.gz emd_27857_half_map_2.map.gz | 112.6 MB 112.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27857 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27857 | HTTPS FTP |
-Validation report
Summary document | emd_27857_validation.pdf.gz | 849.6 KB | Display | EMDB validaton report |
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Full document | emd_27857_full_validation.pdf.gz | 849.2 KB | Display | |
Data in XML | emd_27857_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_27857_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27857 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27857 | HTTPS FTP |
-Related structure data
Related structure data | 8e35MC 8e30C 8e32C 8e33C 8e36C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27857.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.665 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27857_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27857_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 50S E. coli ribosome
+Supramolecule #1: 50S E. coli ribosome
+Macromolecule #1: 23S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 50S ribosomal protein L2
+Macromolecule #4: 50S ribosomal protein L15
+Macromolecule #5: 50S ribosomal protein L4
+Macromolecule #6: 50S ribosomal protein L3
+Macromolecule #7: 50S ribosomal protein L13
+Macromolecule #8: 50S ribosomal protein L22
+Macromolecule #9: 50S ribosomal protein L32
+Macromolecule #10: 50S ribosomal protein L34
+Macromolecule #11: N-{(4R,6R,9S,10R,13S,15aS,17R,20R,22S,24aS)-22-benzyl-6-[3-(4-{[(...
+Macromolecule #12: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 537105 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |