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Yorodumi- EMDB-8646: Locally-refined cryo-EM structure of the small ribosomal subunit ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8646 | |||||||||
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Title | Locally-refined cryo-EM structure of the small ribosomal subunit from Mycobacterium tuberculosis | |||||||||
Map data | small ribosomal subunit from Mycobacterium tuberculosis | |||||||||
Sample |
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Function / homology | Function and homology information small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 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
Map data | emd_8646.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-8646-v30.xml emd-8646.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_8646_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_8646.png | 32.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8646 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8646 | HTTPS FTP |
-Related structure data
Related structure data | 8641C 8645C 8647C 8648C 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_8646.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | small ribosomal subunit from Mycobacterium tuberculosis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.25 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 : 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 / Macromolecule list: #1-#51 |
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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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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.27 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |