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Yorodumi- EMDB-8648: Focused classification of the 70S ribosome from Mycobacterium tub... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8648 | |||||||||
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Title | Focused classification of the 70S ribosome from Mycobacterium tuberculosis | |||||||||
Map data | 70S ribosome from Mycobacterium tuberculosis | |||||||||
Sample |
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Function / homology | Function and homology information large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
Authors | Yang K / Chang J-Y / Cui Z / Zhang J | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2017 Title: Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis. Authors: Kailu Yang / Jeng-Yih Chang / Zhicheng Cui / Xiaojun Li / Ran Meng / Lijun Duan / Jirapat Thongchol / Joanita Jakana / Christoph M Huwe / James C Sacchettini / Junjie Zhang / Abstract: Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the ...Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the 'handle', switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge 'B9'. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs. | |||||||||
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
-Validation report
Summary document | emd_8648_validation.pdf.gz | 408.8 KB | Display | EMDB validaton report |
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Full document | emd_8648_full_validation.pdf.gz | 408.3 KB | Display | |
Data in XML | emd_8648_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | emd_8648_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8648 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8648 | HTTPS FTP |
-Related structure data
Related structure data | 8641C 8645C 8646C 8647C 8649C 5v7qC 5v93C 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_8648.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 70S ribosome from Mycobacterium tuberculosis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.87 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Additional map: 70S ribosome from Mycobacterium tuberculosis
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
+Additional map: Structural analysis of RNA complex
-Sample components
-Entire : Ribosome from human pathogen Mycobacterium tuberculosis
Entire | Name: Ribosome from human pathogen Mycobacterium tuberculosis |
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Components |
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-Supramolecule #1: Ribosome from human pathogen Mycobacterium tuberculosis
Supramolecule | Name: Ribosome from human pathogen Mycobacterium tuberculosis type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) |
-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 TECNAI F20 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.27 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |