[English] 日本語
Yorodumi
- EMDB-61088: Cryo-electron tomography of optogenetically-induced lamellipodia -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61088
TitleCryo-electron tomography of optogenetically-induced lamellipodia
Map data
Sample
  • Cell: lamellipodia in COS-7 cells
Keywordsactin cytoskeleton / plasma membrane / lamellipodia / STRUCTURAL PROTEIN
Biological speciesChlorocebus aethiops (grivet)
Methodelectron tomography / cryo EM
AuthorsInaba H / Imasaki T / Aoyama K / Yoshihara S / Takazaki H / Kato T / Goto H / Mitsuoka K / Nitta R / Nakata T
Funding support Japan, 13 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H05254 Japan
Japan Society for the Promotion of Science (JSPS)18K19328 Japan
Japan Society for the Promotion of Science (JSPS)18K15002 Japan
Japan Society for the Promotion of Science (JSPS)20K16105 Japan
Japan Society for the Promotion of Science (JSPS)22K06219 Japan
Japan Society for the Promotion of Science (JSPS)22K06809 Japan
Japan Society for the Promotion of Science (JSPS)22K20680ZA Japan
Japan Society for the Promotion of Science (JSPS)23K14178ZA Japan
Japan Society for the Promotion of Science (JSPS)23K23823 Japan
Japan Society for the Promotion of Science (JSPS)23K06674 Japan
Japan Agency for Medical Research and Development (AMED)JP21gm161003 Japan
Japan Science and TechnologyJPMJFR214K Japan
Japan Science and TechnologyJPMJMS2024 Japan
CitationJournal: Biorxiv / Year: 2024
Title: Cryo-electron tomography of the actin cytoskeleton and membrane organization during lamellipodia formation using optogenetics.
Authors: Inaba H / Imasaki T / Aoyama K / Yoshihara S / Takazaki H / Kato T / Goto H / Mitsuoka K / Nitta R / Nakata T
History
DepositionAug 6, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_61088.png

Downloads & links

-
Map

FileDownload / File: emd_61088.map.gz / Format: CCP4 / Size: 711.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.85 Å/pix.
x 135 pix.
= 2004.534 Å		14.85 Å/pix.
x 1422 pix.
= 21114.426 Å		14.85 Å/pix.
x 972 pix.
= 14432.645 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: 14.8484 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-1408.29099999999994 - 1127.064599999999928
Average (Standard dev.)-0.5505246 (±57.956142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin851-115
Dimensions1422972135
Spacing9721422135
CellA: 14432.645 Å / B: 21114.426 Å / C: 2004.534 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : lamellipodia in COS-7 cells

EntireName: lamellipodia in COS-7 cells
Components
  • Cell: lamellipodia in COS-7 cells

-
Supramolecule #1: lamellipodia in COS-7 cells

SupramoleculeName: lamellipodia in COS-7 cells / type: cell / ID: 1 / Parent: 0 / Details: PA-Rac1 induced lamellipodia
Source (natural)Organism: Chlorocebus aethiops (grivet) / Organ: kidney

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: SIGMA-Aldrich / Diameter: 20 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.44 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.11.24) / Number images used: 67

+
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