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- EMDB-6473: Platelet from a woman diagnosed with ovarian cancer -

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Basic information

Entry
Database: EMDB / ID: EMD-6473
TitlePlatelet from a woman diagnosed with ovarian cancer
Map dataTomographic reconstruction of a platelet from a woman with an ovarian malignancy
Sample
  • Sample: Tomographic reconstruction of a platelet from a woman with an ovarian malignancy
  • Organelle or cellular component: platelet
Keywordsovarian cancer / platelet / thrombosis / ultrastructure
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsWang R / Stone RL / Kaelber JT / Rochat RH / Nick AM / Vijayan KV / Afshar-Kharghan V / Schmid MF / Dong JF / Sood AK / Chiu W
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
DepositionSep 21, 2015-
Header (metadata) releaseOct 21, 2015-
Map releaseNov 4, 2015-
UpdateJan 20, 2016-
Current statusJan 20, 2016Processing site: RCSB / Status: Released

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Structure visualization

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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
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Supplemental images

emd_6473.png

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Map

FileDownload / File: emd_6473.map.gz / Format: CCP4 / Size: 14.8 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomographic reconstruction of a platelet from a woman with an ovarian malignancy
Voxel sizeX=Y=Z: 14.6 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)5.67059278 (±98.399192810000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00484
Dimensions40964096968
Spacing40964096968
CellA: 59801.6 Å / B: 59801.6 Å / C: 14132.801 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z14.60000048828114.60000048828114.600001033058
M x/y/z40964096968
origin x/y/z0.0000.0000.000
length x/y/z59801.60259801.60214132.801
α/β/γ90.00090.00090.000
start NX/NY/NZ-8211244
NX/NY/NZ115138149
MAP C/R/S123
start NC/NR/NS00484
NC/NR/NS40964096968
D min/max/mean-128.000127.0005.671

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Supplemental data

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Sample components

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Entire : Tomographic reconstruction of a platelet from a woman with an ova...

EntireName: Tomographic reconstruction of a platelet from a woman with an ovarian malignancy
Components
  • Sample: Tomographic reconstruction of a platelet from a woman with an ovarian malignancy
  • Organelle or cellular component: platelet

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Supramolecule #1000: Tomographic reconstruction of a platelet from a woman with an ova...

SupramoleculeName: Tomographic reconstruction of a platelet from a woman with an ovarian malignancy
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: platelet

SupramoleculeName: platelet / type: organelle_or_cellular_component / ID: 1 / Name.synonym: thrombocyte / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Homo sapiens (human) / synonym: human / Tissue: blood / Cell: platelet

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferDetails: native platelet-rich plasma
GridDetails: 200 mesh Quantifoil R3.5/1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: 1 blot, 3 seconds

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Electron microscopy

MicroscopeJEOL 2200FSC
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 10275 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 15.0 µm / Nominal magnification: 8000
Specialist opticsEnergy filter - Name: omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -62 ° / Tilt series - Axis1 - Max angle: 62 ° / Tilt series - Axis1 - Angle increment: 2 °
Alignment procedureLegacy - Astigmatism: objective lens astigmatism correction
Details2 degree tilt increment
DateFeb 10, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 62 / Average electron dose: 2 e/Å2

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD / Number images used: 62

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