[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitlemTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding.
Journal, issue, pagesCell, Vol. 174, Issue 2, Page 338-349.e20, Year 2018
Publish dateJul 12, 2018
AuthorsM Delarue / G P Brittingham / S Pfeffer / I V Surovtsev / S Pinglay / K J Kennedy / M Schaffer / J I Gutierrez / D Sang / G Poterewicz / J K Chung / J M Plitzko / J T Groves / C Jacobs-Wagner / B D Engel / L J Holt /
PubMed AbstractMacromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed ...Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
External linksCell / PubMed:29937223 / PubMed Central
MethodsEM (subtomogram averaging) / EM (tomography)
Resolution11.5 - 26.3 Å
Structure data

EMDB-4372:
Ribosome subtomogram average obtained for control yeast cells
Method: EM (subtomogram averaging) / Resolution: 11.5 Å

EMDB-4373:
Ribosome subtomogram average obtained for yeast cells treated with rapamycin
Method: EM (subtomogram averaging) / Resolution: 11.5 Å

EMDB-4374:
GEM subtomogram average obtained for control yeast cells
Method: EM (subtomogram averaging) / Resolution: 26.3 Å

EMDB-4375:
GEM subtomogram average obtained for yeast cells treated with rapamycin
Method: EM (subtomogram averaging) / Resolution: 26.3 Å

EMDB-4376:
Tomogram obtained for control yeast cells
Method: EM (tomography)

EMDB-4377:
Tomogram obtained for yeast cells treated with rapamycin
Method: EM (tomography)

Source
  • Saccharomyces cerevisiae W303 (yeast)

+
About EMN 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

-
Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

+
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

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

-
EMN Papers

Database of articles cited by 3DEM data entries

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.:EMDB / PDB / Q: What are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

Read more