[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

TitleStructures of EHD2 filaments on curved membranes provide a model for caveolar neck stabilization.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateJul 31, 2026
AuthorsElena Vázquez-Sarandeses / Vasilii Mikirtumov / Jeffrey K Noel / Mikhail Kudryashev / Oliver Daumke /
PubMed AbstractCaveolae are flask-shaped invaginations of the plasma membrane serving critical functions in mechano-protection and signal transduction. Caveolar dynamics, such as caveolar movement within the plasma ...Caveolae are flask-shaped invaginations of the plasma membrane serving critical functions in mechano-protection and signal transduction. Caveolar dynamics, such as caveolar movement within the plasma membrane or endocytosis, relies on precise shaping of the highly curved caveolar necks. The dynamin-like EHD2 ATPase is proposed to oligomerize around the caveolar neck, but its detailed molecular action is poorly understood. Here, we employ cryo-electron tomography to elucidate structures of ring-like EHD2 filaments on tubulated liposomes. EHD2 forms highly curved membrane scaffolds which stabilize a tubular membrane geometry with undulations along the tube's axis, resembling caveolar neck architecture. An amino-terminal sequence facilitates this geometry by acting as a spacer between adjacent filaments. Moreover, in endothelial cells lacking EHD2, caveolar necks become narrower and more elongated. Our structural work provides the molecular framework for understanding EHD2 scaffold formation and its cellular function in caveolar dynamics.
External linksNat Commun / PubMed:42538327 / PubMed Central
MethodsEM (subtomogram averaging)
Resolution6.7 - 10.1 Å
Structure data

53909

9rbu

EMDB-53909, PDB-9rbu:
Cryo-ET structure of full-length membrane-bound EHD2 complex
Method: EM (subtomogram averaging) / Resolution: 6.7 Å

53911

9rc1

EMDB-53911, PDB-9rc1:
Cryo-ET structure of N-terminally truncated membrane-bound EHD2 complex
Method: EM (subtomogram averaging) / Resolution: 10.1 Å

Chemicals

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

Source
  • mus musculus (house mouse)
KeywordsSTRUCTURAL PROTEIN / Eps15-homology domain-containing proteins (EHDs) / dynamin-related ATPases / membrane remodeling / human myotubes / membrane repair process / caveolae / EHD2 / lipid homeostasis / plasma membrane invaginations / oligomer / nucleotide binding / EHD2-dependent caveolae stabilization / GTPase (G-) domain / ATPase activity / liposome tubulation / deltaN / N-terminally truncated

+
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