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- EMDB-8274: YphC and YsxC GTPases assist the maturation of the central protub... -

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Entry
Database: EMDB / ID: 8274
TitleYphC and YsxC GTPases assist the maturation of the central protuberance, GTPase-associated region, and functional core of the 50S ribosomal subunit
Map data50S ribosomal subunit assembly intermediate obtained upon depletion of YsxC protein in Bacillus subtilis
SampleAssembly intermediate of the 50S subunit, Class I:
SourceBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / 5.8 Å resolution
AuthorsNi X / Davis JH / Jain N / Razi A / Benlekbir S / McArthur AG / Rubinstein JR / Britton RA / Williamson JR / Ortega J
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: YphC and YsxC GTPases assist the maturation of the central protuberance, GTPase associated region and functional core of the 50S ribosomal subunit.
Authors: Xiaodan Ni / Joseph H Davis / Nikhil Jain / Aida Razi / Samir Benlekbir / Andrew G McArthur / John L Rubinstein / Robert A Britton / James R Williamson / Joaquin Ortega
Abstract: YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we ...YphC and YsxC are GTPases in Bacillus subtilis that facilitate the assembly of the 50S ribosomal subunit, however their roles in this process are still uncharacterized. To explore their function, we used strains in which the only copy of the yphC or ysxC genes were under the control of an inducible promoter. Under depletion conditions, they accumulated incomplete ribosomal subunits that we named 45SYphC and 44.5SYsxC particles. Quantitative mass spectrometry analysis and the 5-6 Å resolution cryo-EM maps of the 45SYphC and 44.5SYsxC particles revealed that the two GTPases participate in the maturation of the central protuberance, GTPase associated region and key RNA helices in the A, P and E functional sites of the 50S subunit. We observed that YphC and YsxC bind specifically to the two immature particles, suggesting that they represent either on-pathway intermediates or that their structure has not significantly diverged from that of the actual substrate. These results describe the nature of these immature particles, a widely used tool to study the assembly process of the ribosome. They also provide the first insights into the function of YphC and YsxC in 50S subunit assembly and are consistent with this process occurring through multiple parallel pathways, as it has been described for the 30S subunit.
DateDeposition: Jun 30, 2016 / Header (metadata) release: Jul 13, 2016 / Map release: Aug 17, 2016 / Last update: Oct 12, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0218
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0218
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

Fileemd_8274.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.45 Å/pix.
= 348. Å
240 pix
1.45 Å/pix.
= 348. Å
240 pix
1.45 Å/pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:0.0218 (by author), 0.0218 (movie #1):
Minimum - Maximum-0.009929043 - 0.070346676
Average (Standard dev.)0.0011928937 (0.005362565)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 348.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z348.000348.000348.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0100.0700.001

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Supplemental data

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Sample components

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Entire Assembly intermediate of the 50S subunit, Class I

EntireName: Assembly intermediate of the 50S subunit, Class I / Details: Obtained upon depletion of YsxC protein / Number of components: 1

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Component #1: protein, Assembly intermediate of the 50S subunit, Class I

ProteinName: Assembly intermediate of the 50S subunit, Class I / Details: Obtained upon depletion of YsxC protein / Recombinant expression: No
SourceSpecies: Bacillus subtilis (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: Plunged into liquid ethane (FEI VITROBOT MARK III).

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 36033
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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