[English] 日本語
Yorodumi
- EMDB-10449: ER Microsome in Fig. 3 (Martinez et al., Nature Methods) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10449
TitleER Microsome in Fig. 3 (Martinez et al., Nature Methods)
Map dataTomogram with the microsome in Fig. 3 (Martinez et al., Nature Methods)
Sample
  • Organelle or cellular component: Representative tomogram of a canine pancreatic rough Endoplasmic Reticulum vesicle.
Biological speciesCanis lupus familiaris (dog)
Methodelectron tomography / cryo EM
AuthorsMartinez-Sanchez A / Lucic V / Pfeffer S / Forster F
Funding support Spain, 1 items
OrganizationGrant numberCountry
Seneca Foundation Spain
Citation
Journal: Nat Methods / Year: 2020
Title: Template-free detection and classification of membrane-bound complexes in cryo-electron tomograms.
Authors: Antonio Martinez-Sanchez / Zdravko Kochovski / Ulrike Laugks / Johannes Meyer Zum Alten Borgloh / Saikat Chakraborty / Stefan Pfeffer / Wolfgang Baumeister / Vladan Lučić /
Abstract: With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, ...With faithful sample preservation and direct imaging of fully hydrated biological material, cryo-electron tomography provides an accurate representation of molecular architecture of cells. However, detection and precise localization of macromolecular complexes within cellular environments is aggravated by the presence of many molecular species and molecular crowding. We developed a template-free image processing procedure for accurate tracing of complex networks of densities in cryo-electron tomograms, a comprehensive and automated detection of heterogeneous membrane-bound complexes and an unsupervised classification (PySeg). Applications to intact cells and isolated endoplasmic reticulum (ER) allowed us to detect and classify small protein complexes. This classification provided sufficiently homogeneous particle sets and initial references to allow subsequent de novo subtomogram averaging. Spatial distribution analysis showed that ER complexes have different localization patterns forming nanodomains. Therefore, this procedure allows a comprehensive detection and structural analysis of complexes in situ.
#1: Journal: Nature Communications / Year: 2015
Title: Structure of the native Sec61 protein-conducting channel
Authors: Pfeffer S / Forster F
History
DepositionNov 4, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing 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_10449.png

Downloads & links

-
Map

FileDownload / File: emd_10449.map.gz / Format: CCP4 / Size: 10.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram with the microsome in Fig. 3 (Martinez et al., Nature Methods)
Voxel sizeX=Y=Z: 10.48 Å
Density
Minimum - Maximum-0.9645445 - 0.5757894
Average (Standard dev.)-0.0000034647 (±0.0336398)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions159160112
Spacing160159112
CellA: 1676.7999 Å / B: 1666.32 Å / C: 1173.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.4810.4810.48
M x/y/z160159112
origin x/y/z0.0000.0000.000
length x/y/z1676.8001666.3201173.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160159112
D min/max/mean-0.9650.576-0.000

-
Supplemental data

-
Sample components

-
Entire : Representative tomogram of a canine pancreatic rough Endoplasmic ...

EntireName: Representative tomogram of a canine pancreatic rough Endoplasmic Reticulum vesicle.
Components
  • Organelle or cellular component: Representative tomogram of a canine pancreatic rough Endoplasmic Reticulum vesicle.

-
Supramolecule #1: Representative tomogram of a canine pancreatic rough Endoplasmic ...

SupramoleculeName: Representative tomogram of a canine pancreatic rough Endoplasmic Reticulum vesicle.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Canis lupus familiaris (dog) / Tissue: pancreas

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

Concentration2.00 mg/mL
BufferpH: 7.6
Component:
ConcentrationNameFormula
20.0 mMHepes
50.0 mMKCl
2.0 mMMgCl2
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Instrument: FEI VITROBOT MARK IV / Details: Blot 3 seconds before plunging..
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion, Wageningen, The Netherlands / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 42000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: PyTom
Final reconstructionSoftware - Name: PyTom / Number images used: 61
DetailsReconstruction of a single microsome after two binning steps (from 2.62A/pixel to 10.48A/pixel)

+
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