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- EMDB-8593: Subtomogram average of microtubules from Human platelet -

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Basic information

Entry
Database: EMDB / ID: EMD-8593
TitleSubtomogram average of microtubules from Human platelet
Map dataSubtomogram average of microtubules from Human platelet
Sample
  • Organelle or cellular component: Microtubule from Human platelet cells
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 80.0 Å
AuthorsChen M / Wang R / 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: Proc Natl Acad Sci U S A / Year: 2015
Title: Electron cryotomography reveals ultrastructure alterations in platelets from patients with ovarian cancer.
Authors: Rui Wang / Rebecca L Stone / Jason T Kaelber / Ryan H Rochat / Alpa M Nick / K Vinod Vijayan / Vahid Afshar-Kharghan / Michael F Schmid / Jing-Fei Dong / Anil K Sood / Wah Chiu /
Abstract: Thrombocytosis and platelet hyperreactivity are known to be associated with malignancy; however, there have been no ultrastructure studies of platelets from patients with ovarian cancer. Here, we ...Thrombocytosis and platelet hyperreactivity are known to be associated with malignancy; however, there have been no ultrastructure studies of platelets from patients with ovarian cancer. Here, we used electron cryotomography (cryo-ET) to examine frozen-hydrated platelets from patients with invasive ovarian cancer (n = 12) and control subjects either with benign adnexal mass (n = 5) or free from disease (n = 6). Qualitative inspections of the tomograms indicate significant morphological differences between the cancer and control platelets, including disruption of the microtubule marginal band. Quantitative analysis of subcellular features in 120 platelet electron tomograms from these two groups showed statistically significant differences in mitochondria, as well as microtubules. These structural variations in the platelets from the patients with cancer may be correlated with the altered platelet functions associated with malignancy. Cryo-ET of platelets shows potential as a noninvasive biomarker technology for ovarian cancer and other platelet-related diseases.
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: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8593.png

Downloads & links

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Map

FileDownload / File: emd_8593.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of microtubules from Human platelet
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 size
XYZ
EMDB info.121212
CCP4 map header14.314.314.3
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-1.1433123 - 0.80589217
Average (Standard dev.)-0.0020447979 (±0.12463027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin356770567222301317310
Dimensions969696
Spacing969696
CellA=B=C: 1152.0 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 Human platelet cells

EntireName: Microtubule from Human platelet cells
Components
  • Organelle or cellular component: Microtubule from Human platelet cells

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Supramolecule #1: Microtubule from Human platelet cells

SupramoleculeName: Microtubule from Human platelet cells / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Tissue: platelet

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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 2200FS
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: 80.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number subtomograms used: 312
ExtractionNumber tomograms: 1 / Number images used: 312 / Method: Automated tomogram segmentation / Software - Name: EMAN (ver. 2.2)
Final angle assignmentType: NOT APPLICABLE

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