[English] 日本語
Yorodumi
- EMDB-16136: Cryo-electron tomogram acquired on a cryo-FIB lamella of a retina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16136
TitleCryo-electron tomogram acquired on a cryo-FIB lamella of a retinal pigment epithelial (RPE1) cell
Map dataReconstructed cryo-electron tomogram acquired on RPE1 cryo-FIB lamella
Sample
  • Organelle or cellular component: RPE1 cytosol with actin stress fiber
KeywordsActin stress fiber / CYTOSOLIC PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsMahamid J / Goetz SK
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)760067European Union
CitationJournal: Nat Methods / Year: 2020
Title: Tailoring cryo-electron microscopy grids by photo-micropatterning for in-cell structural studies.
Authors: Mauricio Toro-Nahuelpan / Ievgeniia Zagoriy / Fabrice Senger / Laurent Blanchoin / Manuel Théry / Julia Mahamid /
Abstract: Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free ...Spatially controlled cell adhesion on electron microscopy supports remains a bottleneck in specimen preparation for cellular cryo-electron tomography. Here, we describe contactless and mask-free photo-micropatterning of electron microscopy grids for site-specific deposition of extracellular matrix-related proteins. We attained refined cell positioning for micromachining by cryo-focused ion beam milling. Complex micropatterns generated predictable intracellular organization, allowing direct correlation between cell architecture and in-cell three-dimensional structural characterization of the underlying molecular machinery.
History
DepositionNov 14, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16136.png

Downloads & links

-
Map

FileDownload / File: emd_16136.map.gz / Format: CCP4 / Size: 513.3 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationReconstructed cryo-electron tomogram acquired on RPE1 cryo-FIB lamella
Voxel sizeX=Y=Z: 13.481 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-1.4660258 (±27.244865000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00313
Dimensions928928625
Spacing928928625
CellA: 12510.368 Å / B: 12510.368 Å / C: 8425.625 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16136_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : RPE1 cytosol with actin stress fiber

EntireName: RPE1 cytosol with actin stress fiber
Components
  • Organelle or cellular component: RPE1 cytosol with actin stress fiber

-
Supramolecule #1: RPE1 cytosol with actin stress fiber

SupramoleculeName: RPE1 cytosol with actin stress fiber / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: RPE1 cell line / Location in cell: cytosol

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil / Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE
Cryo protectantNone
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 120 / Focused ion beam - Temperature: 88 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Thermo Fisher Aquilos. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 57

+
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