+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6789 | |||||||||
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Title | Large subunit of Mycobacterium smegmatis | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information large ribosomal subunit / ribosomal large subunit assembly / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...large ribosomal subunit / ribosomal large subunit assembly / transferase activity / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Li Z / Ge X / Zhang Y / Zheng L / Sanyal S / Gao N | |||||||||
Citation | Journal: Protein Cell / Year: 2018 Title: Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers. Authors: Zhifei Li / Xueliang Ge / Yixiao Zhang / Lvqin Zheng / Suparna Sanyal / Ning Gao / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6789.map.gz | 9.2 MB | EMDB map data format | |
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Header (meta data) | emd-6789-v30.xml emd-6789.xml | 40.9 KB 40.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6789_fsc.xml | 9.9 KB | Display | FSC data file |
Images | emd_6789.png | 95 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6789 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6789 | HTTPS FTP |
-Validation report
Summary document | emd_6789_validation.pdf.gz | 405.8 KB | Display | EMDB validaton report |
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Full document | emd_6789_full_validation.pdf.gz | 405.3 KB | Display | |
Data in XML | emd_6789_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_6789_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6789 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6789 | HTTPS FTP |
-Related structure data
Related structure data | 5xymMC 6790C 5xyuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6789.map.gz / Format: CCP4 / Size: 83.7 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: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Large subunit of Mycobacterium smegmatis ribosome
+Supramolecule #1: Large subunit of Mycobacterium smegmatis ribosome
+Macromolecule #1: 50S ribosomal protein L32
+Macromolecule #2: 50S ribosomal protein L33 2
+Macromolecule #3: 50S ribosomal protein L34
+Macromolecule #4: 50S ribosomal protein L35
+Macromolecule #5: 50S ribosomal protein L36
+Macromolecule #8: 50S ribosomal protein L2
+Macromolecule #9: 50S ribosomal protein L3
+Macromolecule #10: 50S ribosomal protein L4
+Macromolecule #11: 50S ribosomal protein L5
+Macromolecule #12: 50S ribosomal protein L6
+Macromolecule #13: 50S ribosomal protein L9
+Macromolecule #14: 50S ribosomal protein L13
+Macromolecule #15: 50S ribosomal protein L14
+Macromolecule #16: 50S ribosomal protein L15
+Macromolecule #17: 50S ribosomal protein L16
+Macromolecule #18: 50S ribosomal protein L17
+Macromolecule #19: 50S ribosomal protein L18
+Macromolecule #20: 50S ribosomal protein L19
+Macromolecule #21: 50S ribosomal protein L20
+Macromolecule #22: 50S ribosomal protein L21
+Macromolecule #23: 50S ribosomal protein L22
+Macromolecule #24: 50S ribosomal protein L23
+Macromolecule #25: 50S ribosomal protein L24
+Macromolecule #26: 50S ribosomal protein L25
+Macromolecule #27: 50S ribosomal protein L27
+Macromolecule #28: 50S ribosomal protein L28
+Macromolecule #29: 50S ribosomal protein L29
+Macromolecule #30: 50S ribosomal protein L30
+Macromolecule #31: Uncharacterized protein bL37
+Macromolecule #6: 23S RNA
+Macromolecule #7: 5S RNA
+Macromolecule #32: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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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 K2 SUMMIT (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |