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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6472 | |||||||||
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Title | Platelet from a woman with benign ovarian mass | |||||||||
![]() | Tomographic reconstruction of a platelet from a woman with a benign ovarian mass | |||||||||
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![]() | ovarian cancer / platelet / thrombosis / ultrastructure | |||||||||
Biological species | ![]() | |||||||||
Method | electron tomography / cryo EM | |||||||||
![]() | Wang R / Stone RL / Kaelber JT / Rochat RH / Nick AM / Vijayan KV / Afshar-Kharghan V / Schmid MF / Dong JF / Sood AK / Chiu W | |||||||||
![]() | ![]() 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. | |||||||||
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 7.6 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.2 KB 9.2 KB | Display Display | ![]() |
Images | ![]() | 298.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 78.3 KB | Display | ![]() |
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Full document | ![]() | 77.4 KB | Display | |
Data in XML | ![]() | 499 B | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Tomographic reconstruction of a platelet from a woman with a benign ovarian mass | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Tomographic reconstruction of a platelet from a woman with a beni...
Entire | Name: Tomographic reconstruction of a platelet from a woman with a benign ovarian mass |
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Components |
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-Supramolecule #1000: Tomographic reconstruction of a platelet from a woman with a beni...
Supramolecule | Name: Tomographic reconstruction of a platelet from a woman with a benign ovarian mass type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: platelet
Supramolecule | Name: platelet / type: organelle_or_cellular_component / ID: 1 / Name.synonym: thrombocyte / Number of copies: 1 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | electron tomography |
Aggregation state | cell |
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Sample preparation
Buffer | Details: native platelet-rich plasma |
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Grid | Details: 200 mesh Quantifoil R3.5/1 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: 1 blot, 3 seconds |
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Electron microscopy
Microscope | JEOL 2200FSC |
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Alignment procedure | Legacy - Astigmatism: objective lens astigmatism correction |
Specialist optics | Energy filter - Name: omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV |
Details | 2 degree tilt increment |
Date | Jun 11, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 62 / Average electron dose: 2 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 12500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 12.0 µm / Nominal magnification: 10000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -62 ° / Tilt series - Axis1 - Max angle: 62 ° / Tilt series - Axis1 - Angle increment: 2 ° |
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Image processing
Final reconstruction | Algorithm: OTHER / Software - Name: ![]() |
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