[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleThe molecular basis of tricalbin-mediated membrane contact site organization in cells.
Journal, issue, pagesJ Cell Sci, Vol. 139, Issue 9, Year 2026
Publish dateMay 1, 2026
AuthorsLazar Ivanović / Anne-Laure Boinet / Andrea Picco / Eliane Zinn / Daniela Ross-Kaschitza / Marko Kaksonen / Wanda Kukulski /
PubMed AbstractMembrane contact sites facilitate molecular exchanges through physical interactions between organelles, connected by specific protein tethers. Among these tethers are the tricalbins, which mediate ...Membrane contact sites facilitate molecular exchanges through physical interactions between organelles, connected by specific protein tethers. Among these tethers are the tricalbins, which mediate contacts between endoplasmic reticulum (ER) and plasma membrane in yeast. Tricalbins are integral to the ER, have a cytosolic lipid-binding domain and bind the plasma membrane through C2 domains. Here, we combine fluorescence recovery after photobleaching with correlative light and 3D electron microscopy to dissect how tricalbins control their localization, dynamic distribution and contact site organization. We find that heteromerization via lipid-binding domains is a prerequisite for tricalbin accumulation at contact sites, membrane curvature sensing and restrained mobility in the ER. By altering tricalbin protein domains, we show that intermembrane distances and intrinsically disordered regions interdependently control distribution and dynamics of contact site tethers. Our study reveals principles of contact site architecture that are fine-tuned by tricalbin domain organization.
External linksJ Cell Sci / PubMed:41948883
MethodsEM (tomography)
Structure data

EMDB-57516: Electron tomogram of resin-embedded wild type yeast cells expressing Tcb3(1-490)-chimeraC-GFP
Method: EM (tomography)

EMDB-57517: Electron tomogram of resin-embedded yeast cells expressing Tcb3(1-490)-chimeraC-GFP, deleted for tcb1/2
Method: EM (tomography)

EMDB-57518: Electron tomogram of resin-embedded yeast cells expressing Tcb3(1-490)-chimeraC-GFP, deleted for tcb1/2, scs2/22 and ist2
Method: EM (tomography)

EMDB-57519: Electron tomogram of resin-embedded yeast cells expressing Tcb3(1-272)-chimeraC-GFP, deleted for tcb1/2, scs2/22 and ist2
Method: EM (tomography)

EMDB-57520: Electron tomogram of resin-embedded yeast cells expressing Tcb3(1-272)-GFP-chimeraC, deleted for tcb1/2, scs2/22 and ist2
Method: EM (tomography)

EMDB-57521: Electron tomogram of resin-embedded yeast cells expressing Tcb3(191-490)-GFP-chimeraC, deleted for tcb1/2, scs2/22 and ist2
Method: EM (tomography)

EMDB-57522: Electron tomogram of resin-embedded yeast cells expressing Tcb3(191-272)-chimeraC-GFP, deleted for tcb1/2, scs2/22 and ist2
Method: EM (tomography)

EMDB-57523: Cryo-electron tomogram of yeast cells expressing Tcb3(191-490)-chimeraC-GFP, deleted for tcb1/2, scs2/22 and ist2.
Method: EM (tomography)

Source
  • Saccharomyces cerevisiae (brewer's yeast)

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more