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- EMDB-0400: Electron microscopy snapshots of single particles from single cells -

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Basic information

Entry
Database: EMDB / ID: EMD-0400
TitleElectron microscopy snapshots of single particles from single cells
Map dataReconstruction of 80S ribosome
Sample
  • Complex: 80S ribosome from single cells
Biological speciesCaenorhabditis elegans (invertebrata)
Methodsingle particle reconstruction / negative staining / Resolution: 45.0 Å
AuthorsYi X / Verbeke EJ / Yiran C / Dickinson DJ / Taylor DW
Funding support United States, 2 items
OrganizationGrant numberCountry
Robert A. Welch FoundationF-1938 United States
National Institutes of Health/National Human Genome Research InstituteR00 GM115964 United States
CitationJournal: J Biol Chem / Year: 2019
Title: Electron microscopy snapshots of single particles from single cells.
Authors: Xiunan Yi / Eric J Verbeke / Yiran Chang / Daniel J Dickinson / David W Taylor /
Abstract: Cryo-electron microscopy (cryo-EM) has become an indispensable tool for structural studies of biological macromolecules. Two additional predominant methods are available for studying the ...Cryo-electron microscopy (cryo-EM) has become an indispensable tool for structural studies of biological macromolecules. Two additional predominant methods are available for studying the architectures of multiprotein complexes: 1) single-particle analysis of purified samples and 2) tomography of whole cells or cell sections. The former can produce high-resolution structures but is limited to highly purified samples, whereas the latter can capture proteins in their native state but has a low signal-to-noise ratio and yields lower-resolution structures. Here, we present a simple, adaptable method combining microfluidic single-cell extraction with single-particle analysis by EM to characterize protein complexes from individual embryos. Using this approach, we uncover 3D structures of ribosomes directly from single embryo extracts. Moreover, we investigated structural dynamics during development by counting the number of ribosomes per polysome in early and late embryos. This approach has significant potential applications for counting protein complexes and studying protein architectures from single cells in developmental, evolutionary, and disease contexts.
History
DepositionDec 6, 2018-
Header (metadata) releaseDec 19, 2018-
Map releaseDec 19, 2018-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0400.png

Downloads & links

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Map

FileDownload / File: emd_0400.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of 80S ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.6 Å/pix.
x 160 pix.
= 576. Å		3.6 Å/pix.
x 160 pix.
= 576. Å		3.6 Å/pix.
x 160 pix.
= 576. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.031031292 - 0.08494407
Average (Standard dev.)0.00024659812 (±0.004081533)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 576.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.63.63.6
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z576.000576.000576.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0310.0850.000

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Supplemental data

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Sample components

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Entire : 80S ribosome from single cells

EntireName: 80S ribosome from single cells
Components
  • Complex: 80S ribosome from single cells

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Supramolecule #1: 80S ribosome from single cells

SupramoleculeName: 80S ribosome from single cells / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 1 MDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate
GridDetails: unspecified

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Electron microscopy

MicroscopeJEOL 2010F
Image recordingFilm or detector model: GATAN MULTISCAN / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 9000
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 45.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 2000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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