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- EMDB-6178: CryoEM map of Mycobacterium tuberculosis 50S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-6178
TitleCryoEM map of Mycobacterium tuberculosis 50S ribosome
Map dataMycobacterium tuberculosis 50S ribosome
Sample
  • Sample: Mycobacterium tuberculosis ribosome 50S
  • Complex: 50S ribosomeProkaryotic large ribosomal subunit
KeywordsMycobacterium tuberculosis / ribosome / 50S
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsYang K / Zhang J
CitationJournal: 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
DepositionNov 6, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseAug 26, 2015-
UpdateOct 14, 2015-
Current statusOct 14, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_6178.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMycobacterium tuberculosis 50S ribosome
Voxel sizeX=Y=Z: 1.85 Å
Density
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.05872771 - 0.24779128
Average (Standard dev.)0.00658154 (±0.02942729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.851.851.85
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z355.200355.200355.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0590.2480.007

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Supplemental data

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Sample components

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Entire : Mycobacterium tuberculosis ribosome 50S

EntireName: Mycobacterium tuberculosis ribosome 50S
Components
  • Sample: Mycobacterium tuberculosis ribosome 50S
  • Complex: 50S ribosomeProkaryotic large ribosomal subunit

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Supramolecule #1000: Mycobacterium tuberculosis ribosome 50S

SupramoleculeName: Mycobacterium tuberculosis ribosome 50S / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: 1 / Number unique components: 1
Molecular weightExperimental: 1.6 MDa / Theoretical: 1.6 MDa

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Supramolecule #1: 50S ribosome

SupramoleculeName: 50S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI
Ribosome-details: ribosome-prokaryote: LSU 50S, LSU RNA 23S, LSU RNA 5S
Source (natural)Organism: Mycobacterium tuberculosis (bacteria) / Strain: MC_2 7000
Molecular weightTheoretical: 1.6 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.6 mg/mL
BufferpH: 7.5
Details: 5 mM HEPES sodium, pH 7.5, 10 mM NH4Cl, 50 mM KCl, 10 mM MgCl2
GridDetails: 200 mesh R2/2 Quantifoil grid, glow-discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 81081 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 62000
Sample stageSpecimen holder: 626 holder / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 100 K
DateAug 6, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 165 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: OTHER / Software - Name: CTFFIND3, EMAN2.1, RELION1.3 / Number images used: 21287
DetailsImages processed with CTFFIND3, EMAN2.1, and RELION1.3.
FSC plot (resolution estimation)

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