[English] 日本語
Yorodumi
- EMDB-6471: Platelet from a healthy woman -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6471
TitlePlatelet from a healthy woman
Map dataTomographic reconstruction of a platelet from a healthy donor
Sample
  • Sample: Tomographic reconstruction of a platelet from a healthy donor
  • 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-
UpdateNov 11, 2015-
Current statusNov 11, 2015Processing site: RCSB / Status: Released

-
Structure visualization

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

emd_6471.png

Downloads & links

-
Map

FileDownload / File: emd_6471.map.gz / Format: CCP4 / Size: 4.9 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomographic reconstruction of a platelet from a healthy donor
Voxel sizeX=Y=Z: 12 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)7.05368996 (±86.030555730000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-282-896200
Dimensions34203135500
Spacing34203135500
CellA: 37620.0 Å / B: 41040.0 Å / C: 6000.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z121212
M x/y/z31353420500
origin x/y/z0.0000.0000.000
length x/y/z37620.00041040.0006000.000
α/β/γ90.00090.00090.000
start NX/NY/NZ46-111107
NX/NY/NZ131164142
MAP C/R/S123
start NC/NR/NS-896-282200
NC/NR/NS31353420500
D min/max/mean-128.000127.0007.054

-
Supplemental data

-
Sample components

-
Entire : Tomographic reconstruction of a platelet from a healthy donor

EntireName: Tomographic reconstruction of a platelet from a healthy donor
Components
  • Sample: Tomographic reconstruction of a platelet from a healthy donor
  • Organelle or cellular component: platelet

-
Supramolecule #1000: Tomographic reconstruction of a platelet from a healthy donor

SupramoleculeName: Tomographic reconstruction of a platelet from a healthy donor
type: sample / ID: 1000 / Number unique components: 1

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
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: 2 blots, 2 seconds each

-
Electron microscopy

MicroscopeJEOL 2200FSC
Alignment procedureLegacy - Astigmatism: objective lens astigmatism correction
Specialist opticsEnergy filter - Name: omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV
Details2 degree tilt increment
DateOct 11, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 62 / Average electron dose: 2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 12500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 15.0 µm / Nominal magnification: 10000
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 °

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more