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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6177 | |||||||||
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Title | CryoEM map of Mycobacterium tuberculosis 50S ribosome with RsfS | |||||||||
![]() | Mycobacterium tuberculosis 50S ribosome bound with RsfS | |||||||||
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![]() | Mycobacterium tuberculosis / ribosome / silencing factor | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.1 Å | |||||||||
![]() | Yang K / Zhang J | |||||||||
![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10 KB 10 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.1 KB | Display | ![]() |
Images | ![]() ![]() | 58.8 KB 4.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.6 KB | Display | ![]() |
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Full document | ![]() | 77.7 KB | Display | |
Data in XML | ![]() | 493 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Mycobacterium tuberculosis 50S ribosome bound with RsfS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Mycobacterium Tuberculosis ribosome 50S bound with RsfS
Entire | Name: Mycobacterium Tuberculosis ribosome 50S bound with RsfS |
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Components |
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-Supramolecule #1000: Mycobacterium Tuberculosis ribosome 50S bound with RsfS
Supramolecule | Name: Mycobacterium Tuberculosis ribosome 50S bound with RsfS type: sample / ID: 1000 / Details: The sample was monodisperse. / Oligomeric state: One RsfS binds to one ribosome 50S / Number unique components: 2 |
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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: ![]() ![]() |
Molecular weight | Theoretical: 1.6 MDa |
-Macromolecule #1: Ribosomal silencing factor RsfS
Macromolecule | Name: Ribosomal silencing factor RsfS / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |