+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6178 | |||||||||
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Title | CryoEM map of Mycobacterium tuberculosis 50S ribosome | |||||||||
Map data | Mycobacterium tuberculosis 50S ribosome | |||||||||
Sample |
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Keywords | Mycobacterium tuberculosis / ribosome / 50S | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.3 Å | |||||||||
Authors | Yang K / Zhang J | |||||||||
Citation | Journal: Structure / Year: 2015 Title: Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome. Authors: Xiaojun Li / Qingan Sun / Cai Jiang / Kailu Yang / Li-Wei Hung / Junjie Zhang / James C Sacchettini / Abstract: The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) ...The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) RsfS, together with the cryo-electron microscopy (EM) structure of the large subunit 50S of Mtb ribosome, reveals how inhibition of protein synthesis by RsfS occurs. RsfS binds to the 50S at L14, which, when occupied, blocks the association of the small subunit 30S. Although Mtb RsfS is a dimer in solution, only a single subunit binds to 50S. The overlap between the dimer interface and the L14 binding interface confirms that the RsfS dimer must first dissociate to a monomer in order to bind to L14. RsfS interacts primarily through electrostatic and hydrogen bonding to L14. The EM structure shows extended rRNA density that it is not found in the Escherichia coli ribosome, the most striking of these being the extended RNA helix of H54a. | |||||||||
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_6178.map.gz | 8.5 MB | EMDB map data format | |
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Header (meta data) | emd-6178-v30.xml emd-6178.xml | 9.1 KB 9.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_6178_fsc.xml | 7.1 KB | Display | FSC data file |
Images | 400_6178.gif 80_6178.gif | 55.7 KB 4.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6178 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6178 | HTTPS FTP |
-Validation report
Summary document | emd_6178_validation.pdf.gz | 78.9 KB | Display | EMDB validaton report |
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Full document | emd_6178_full_validation.pdf.gz | 78 KB | Display | |
Data in XML | emd_6178_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6178 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6178 | HTTPS FTP |
-Related 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_6178.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mycobacterium tuberculosis 50S ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.85 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 : Mycobacterium tuberculosis ribosome 50S
Entire | Name: Mycobacterium tuberculosis ribosome 50S |
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Components |
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-Supramolecule #1000: Mycobacterium tuberculosis ribosome 50S
Supramolecule | Name: Mycobacterium tuberculosis ribosome 50S / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: 1 / Number unique components: 1 |
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Molecular weight | Experimental: 1.6 MDa / Theoretical: 1.6 MDa |
-Supramolecule #1: 50S ribosome
Supramolecule | Name: 50S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S |
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Source (natural) | Organism: Mycobacterium tuberculosis (bacteria) / Strain: MC_2 7000 |
Molecular weight | Theoretical: 1.6 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.5 Details: 5 mM HEPES sodium, pH 7.5, 10 mM NH4Cl, 50 mM KCl, 10 mM MgCl2 |
Grid | Details: 200 mesh R2/2 Quantifoil grid, glow-discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 100 K |
Date | Aug 6, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 165 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 81081 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder: 626 holder / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |