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

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Basic information

Entry
Database: EMDB / ID: EMD-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
Sample
  • Complex: Assembly intermediate of the 50S subunit, Class I
KeywordsRibosome assembly / 50S subunit / YsxC protein / RIBOSOME
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsNi X / Davis JH / Jain N / Razi A / Benlekbir S / McArthur AG / Rubinstein JR / Britton RA / Williamson JR / Ortega J
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research[MOP-82930] Canada
National Science and Engineering Research Council of Canada[RGPIN288327-07] Canada
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.
History
DepositionJun 30, 2016-
Header (metadata) releaseJul 13, 2016-
Map releaseAug 17, 2016-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

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

emd_8274.png

Downloads & links

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Map

FileDownload / File: emd_8274.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation50S ribosomal subunit assembly intermediate obtained upon depletion of YsxC protein in Bacillus subtilis
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0218 / Movie #1: 0.0218
Minimum - Maximum-0.009929043 - 0.070346676
Average (Standard dev.)0.0011928937 (±0.005362565)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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/NZ000
NX/NY/NZ288288288
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
Components
  • Complex: Assembly intermediate of the 50S subunit, Class I

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

SupramoleculeName: Assembly intermediate of the 50S subunit, Class I / type: complex / ID: 1 / Parent: 0 / Details: Obtained upon depletion of YsxC protein
Source (natural)Organism: Bacillus subtilis (bacteria)

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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

BufferpH: 7.5
GridModel: C-flats CFT-222C / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III
Details: Plunged into liquid ethane (FEI VITROBOT MARK III).

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.5 sec. / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36033
FSC plot (resolution estimation)

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