[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

TitleTricalbins Contribute to Cellular Lipid Flux and Form Curved ER-PM Contacts that Are Bridged by Rod-Shaped Structures.
Journal, issue, pagesDev Cell, Vol. 51, Issue 4, Page 488-502.e8, Year 2019
Publish dateNov 18, 2019
AuthorsPatrick C Hoffmann / Tanmay A M Bharat / Michael R Wozny / Jerome Boulanger / Elizabeth A Miller / Wanda Kukulski /
PubMed AbstractLipid flow between cellular organelles occurs via membrane contact sites. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and ...Lipid flow between cellular organelles occurs via membrane contact sites. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and plasma membrane (PM). How these proteins regulate membrane architecture to transport lipids across the aqueous space between bilayers remains unknown. Using correlative microscopy, electron cryo-tomography, and high-throughput genetics, we address the interplay of architecture and function in budding yeast. We find that ER-PM contacts differ in protein composition and membrane morphology, not in intermembrane distance. In situ electron cryo-tomography reveals the molecular organization of tricalbin-mediated contacts, suggesting a structural framework for putative lipid transfer. Genetic analysis uncovers functional overlap with cellular lipid routes, such as maintenance of PM asymmetry. Further redundancies are suggested for individual tricalbin protein domains. We propose a modularity of molecular and structural functions of tricalbins and of their roles within the cellular network of lipid distribution pathways.
External linksDev Cell / PubMed:31743663 / PubMed Central
MethodsEM (tomography)
Structure data

EMDB-10287:
CLEM of resin-embedded GFP-Scs2 yeast cell shown in Figure 2A of publication
Method: EM (tomography)

EMDB-10299:
CLEM of resin-embedded GFP-Ist2 yeast cell shown in Figure 2B of publication
Method: EM (tomography)

EMDB-10300:
CLEM of resin-embedded Tcb3-GFP yeast cell shown in Figure 2C of publication
Method: EM (tomography)

EMDB-10301:
CLEM of resin-embedded scs2/22 tcb1/2/3 deletion mutant yeast cell expressing GFP-Ist2 shown in Figure 2F of publication
Method: EM (tomography)

EMDB-10302:
CLEM of resin-embedded scs2/22 ist2 deletion mutant yeast cell expressing Tcb3-GFP; shown in Figure 2G of publication
Method: EM (tomography)

EMDB-10303:
CLEM of resin-embedded scs2/22 ist2 tcb1/2/3 deletion mutant yeast cell expressing Sec63-RFP from plasmid, shown in Figure 2H of publication
Method: EM (tomography)

EMDB-10304:
CLEM of resin-embedded rtn1 yop1 deletion mutant yeast cell expressing Tcb3-GFP, shown in Figure 3C of publication
Method: EM (tomography)

EMDB-10306:
CLEM of resin-embedded rtn1 yop1 deletion mutant yeast cell expressing Tcb3-GFP, shown in Figure 3E of publication
Method: EM (tomography)

EMDB-10308:
cryo-ET of cryo-FIB milled yeast cell in which scs2/22 ist2 are deleted; shown in Figures 5A and S3B of publication
Method: EM (tomography)

EMDB-10309:
cryo-ET of cryo-FIB milled yeast cell, in which scs2/22 ist2 are deleted, with high intracellular calcium; shown in Figures 5C and S3F
Method: EM (tomography)

EMDB-10310:
cryo-ET of cryo-FIB milled yeast cell, in which Tcb3-GFP is overexpressed and scs2/22 ist2 tcb1/2 are deleted; shown in Figure 6 of publication
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