[English] 日本語
Yorodumi
- EMDB-52503: Cryo-tomogram of fascin-actin bundles reconstituted in vitro -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52503
TitleCryo-tomogram of fascin-actin bundles reconstituted in vitro
Map data
Sample
  • Complex: Purified fascin mixed with purified actin filaments
    • Organelle or cellular component: fascin protein
    • Organelle or cellular component: actin filament
Keywordsfascin / actin-binding protein / actin filaments / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsSong X / Corbalan-Garcia S / Huiskonen JT
Funding support Finland, 1 items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation Finland
CitationJournal: J Struct Biol / Year: 2025
Title: The mechanism underlying fascin-mediated bundling of actin filaments unveiled by cryo-electron tomography.
Authors: Xiyong Song / Jesús Baltanás-Copado / Muniyandi Selvaraj / Shrikant B Kokate / Esa-Pekka Kumpula / Senena Corbalán-García / Juha T Huiskonen /
Abstract: Fascins are crucial actin-binding proteins linked to carcinomas, such as cancer metastasis. Fascins crosslink unipolar actin filaments into linear and rigid parallel bundles, which play essential ...Fascins are crucial actin-binding proteins linked to carcinomas, such as cancer metastasis. Fascins crosslink unipolar actin filaments into linear and rigid parallel bundles, which play essential roles in the formation of filopodia, stereocilia and other membrane protrusions. However, the mechanism of how fascin bundles actin filaments has remained elusive. Here, we studied the organization of reconstituted fascin-actin bundles by cryo-electron tomography and determined the structure of the fascin-actin complex at 9 Å resolution by subtomogram averaging. Consistent with earlier findings, fascin molecules decorate adjacent actin filaments, positioned at regular intervals corresponding to the half-pitch of actin filaments. The fascin-actin complex structure allows us to verify the binding orientation of fascin between the two actin filaments. Fitting of the previously solved fascin crystal structure facilitates the analysis of the interaction surfaces. Our structural models serve as a blueprint to understand the detailed interactions between fascin and actins and provide new insights for the development of drugs targeting fascin proteins.
History
DepositionJan 9, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52503.png

Downloads & links

-
Map

FileDownload / File: emd_52503.map.gz / Format: CCP4 / Size: 953.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.17 Å/pix.
x 250 pix.
= 1543. Å		6.17 Å/pix.
x 1000 pix.
= 6172. Å		6.17 Å/pix.
x 1000 pix.
= 6172. 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: 6.172 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.3298521 - 0.50919235
Average (Standard dev.)0.0000030922822 (±0.015701013)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10001000250
Spacing10001000250
CellA: 6172.0 Å / B: 6172.0 Å / C: 1543.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Purified fascin mixed with purified actin filaments

EntireName: Purified fascin mixed with purified actin filaments
Components
  • Complex: Purified fascin mixed with purified actin filaments
    • Organelle or cellular component: fascin protein
    • Organelle or cellular component: actin filament

-
Supramolecule #1: Purified fascin mixed with purified actin filaments

SupramoleculeName: Purified fascin mixed with purified actin filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: fascin protein

SupramoleculeName: fascin protein / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: actin filament

SupramoleculeName: actin filament / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: Warp (ver. v1.1.0) / Number images used: 41
CTF correctionSoftware - Name: Warp (ver. v1.1.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

+
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