[English] 日本語
Yorodumi
- EMDB-10766: Tomogram of a mouse neuron including segmentation of the Golgi ap... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10766
TitleTomogram of a mouse neuron including segmentation of the Golgi apparatus and the spherical vesicles for validating a curvature estimation algorithm.
Map dataRaw tomogram.
Sample
  • Organelle or cellular component: Neurons from cortical mouse tissue cultured 7 days in vitro.
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsSchaefer T / Salfer M
Funding support Germany, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)FP7 GA ERC-2012-387 SyG_318987-ToPAG Germany
German Research Foundation (DFG)GSC-1006 Germany
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
CitationJournal: PLoS Comput Biol / Year: 2020
Title: Reliable estimation of membrane curvature for cryo-electron tomography.
Authors: Maria Salfer / Javier F Collado / Wolfgang Baumeister / Rubén Fernández-Busnadiego / Antonio Martínez-Sánchez /
Abstract: Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to- ...Curvature is a fundamental morphological descriptor of cellular membranes. Cryo-electron tomography (cryo-ET) is particularly well-suited to visualize and analyze membrane morphology in a close-to-native state and molecular resolution. However, current curvature estimation methods cannot be applied directly to membrane segmentations in cryo-ET, as these methods cannot cope with some of the artifacts introduced during image acquisition and membrane segmentation, such as quantization noise and open borders. Here, we developed and implemented a Python package for membrane curvature estimation from tomogram segmentations, which we named PyCurv. From a membrane segmentation, a signed surface (triangle mesh) is first extracted. The triangle mesh is then represented by a graph, which facilitates finding neighboring triangles and the calculation of geodesic distances necessary for local curvature estimation. PyCurv estimates curvature based on tensor voting. Beside curvatures, this algorithm also provides robust estimations of surface normals and principal directions. We tested PyCurv and three well-established methods on benchmark surfaces and biological data. This revealed the superior performance of PyCurv not only for cryo-ET, but also for data generated by other techniques such as light microscopy and magnetic resonance imaging. Altogether, PyCurv is a versatile open-source software to reliably estimate curvature of membranes and other surfaces in a wide variety of applications.
History
DepositionMar 15, 2020-
Header (metadata) releaseAug 5, 2020-
Map releaseAug 5, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / 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_10766.png

Downloads & links

-
Map

FileDownload / File: emd_10766.map.gz / Format: CCP4 / Size: 410.6 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationRaw tomogram.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
16.84 Å/pix.
x 250 pix.
= 4210. Å		16.84 Å/pix.
x 928 pix.
= 15627.521 Å		16.84 Å/pix.
x 928 pix.
= 15627.521 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 16.84 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-3787.0 - 1761.0
Average (Standard dev.)146.68971 (±219.56316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00125
Dimensions928928250
Spacing928928250
CellA: 15627.5205 Å / B: 15627.5205 Å / C: 4210.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z16.84000107758616.84000107758616.84
M x/y/z928928250
origin x/y/z0.0000.0000.000
length x/y/z15627.52115627.5214210.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS00125
NC/NR/NS928928250
D min/max/mean-3787.0001761.000146.690

-
Supplemental data

-
Mask #1

Fileemd_10766_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_10766_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Filtered tomogram using a deconvolution filter (https://github.com/dtegunov/tom deconv) executed...

Fileemd_10766_additional.map
AnnotationFiltered tomogram using a deconvolution filter (https://github.com/dtegunov/tom_deconv) executed in MATLAB (Mathworks) using the functionalities of the TOM toolbox (Nickel et al. 2005).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Filtered tomogram using a deconvolution filter (https://github.com/dtegunov/tom deconv) executed...

Fileemd_10766_additional_1.map
AnnotationFiltered tomogram using a deconvolution filter (https://github.com/dtegunov/tom_deconv) executed in MATLAB (Mathworks) using the functionalities of the TOM toolbox (Nickel et al. 2005).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Neurons from cortical mouse tissue cultured 7 days in vitro.

EntireName: Neurons from cortical mouse tissue cultured 7 days in vitro.
Components
  • Organelle or cellular component: Neurons from cortical mouse tissue cultured 7 days in vitro.

-
Supramolecule #1: Neurons from cortical mouse tissue cultured 7 days in vitro.

SupramoleculeName: Neurons from cortical mouse tissue cultured 7 days in vitro.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE-PROPANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.03 nA / Focused ion beam - Duration: 4000 sec. / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 1000 nm / Focused ion beam - Final thickness: 200 nm
Focused ion beam - Details: The value given for _emd_sectioning_focused_ion_beam.instrument is Quanta 3D Cryo-FIB / SEM. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K / Max: 90.0 K
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
DetailsAlso phase plate alignment.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.1 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 60

+
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