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- EMDB-8592: Subtomogram average of microtubules from PC12 cell -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-8592
TitleSubtomogram average of microtubules from PC12 cell
Map data
Sample
  • Organelle or cellular component: Microtubule from PC12 cells
Biological speciesRattus (rat)
Methodsubtomogram averaging / cryo EM / Resolution: 64.0 Å
AuthorsChen M / Dai W / Schmid MF / Chiu W / Ludtke SJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080139, P01NS092525, P41GM103832 United States
CitationJournal: Nat Methods / Year: 2017
Title: Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.
Authors: Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke /
Abstract: Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components ...Cellular electron cryotomography offers researchers the ability to observe macromolecules frozen in action in situ, but a primary challenge with this technique is identifying molecular components within the crowded cellular environment. We introduce a method that uses neural networks to dramatically reduce the time and human effort required for subcellular annotation and feature extraction. Subsequent subtomogram classification and averaging yield in situ structures of molecular components of interest. The method is available in the EMAN2.2 software package.
History
DepositionFeb 3, 2017-
Header (metadata) releaseMar 1, 2017-
Map releaseMar 1, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8592.png

Downloads & links

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Map

FileDownload / File: emd_8592.map.gz / Format: CCP4 / Size: 432.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.3 Å/pix.
x 48 pix.
= 686.4 Å		14.3 Å/pix.
x 48 pix.
= 686.4 Å		14.3 Å/pix.
x 48 pix.
= 686.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 14.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-1.6776736 - 1.7911501
Average (Standard dev.)-0.0029733914 (±0.28868338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-24-24-24
Dimensions484848
Spacing484848
CellA=B=C: 686.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z14.314.314.3
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z686.400686.400686.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-24-24-24
NC/NR/NS484848
D min/max/mean-1.6781.791-0.003

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Supplemental data

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Sample components

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Entire : Microtubule from PC12 cells

EntireName: Microtubule from PC12 cells
Components
  • Organelle or cellular component: Microtubule from PC12 cells

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Supramolecule #1: Microtubule from PC12 cells

SupramoleculeName: Microtubule from PC12 cells / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Rattus (rat) / Tissue: adrenal medulla

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2100
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 2.0 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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 64.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number subtomograms used: 677
ExtractionNumber tomograms: 1 / Number images used: 677 / Method: Automated tomogram segmentation / Software - Name: EMAN (ver. 2.1)
Final angle assignmentType: NOT APPLICABLE

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