[English] 日本語
Yorodumi
- PDB-9rbu: Cryo-ET structure of full-length membrane-bound EHD2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9rbu
TitleCryo-ET structure of full-length membrane-bound EHD2 complex
ComponentsEH domain-containing protein 2
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
Function / homology
Function and homology information


positive regulation of endocytic recycling / plasma membrane tubulation / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / positive regulation of myoblast fusion / endocytic vesicle / cilium assembly / protein localization to plasma membrane / caveola ...positive regulation of endocytic recycling / plasma membrane tubulation / Factors involved in megakaryocyte development and platelet production / endocytic recycling / cortical actin cytoskeleton organization / positive regulation of myoblast fusion / endocytic vesicle / cilium assembly / protein localization to plasma membrane / caveola / endocytosis / recycling endosome membrane / early endosome / protein-macromolecule adaptor activity / protein domain specific binding / hydrolase activity / calcium ion binding / GTP binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
EH domain-containing protein, N-terminal / Domain of unknown function DUF5600 / N-terminal EH-domain containing protein / Domain of unknown function (DUF5600) / EH domain / EH domain profile. / Eps15 homology domain / EH domain / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. ...EH domain-containing protein, N-terminal / Domain of unknown function DUF5600 / N-terminal EH-domain containing protein / Domain of unknown function (DUF5600) / EH domain / EH domain profile. / Eps15 homology domain / EH domain / Dynamin-type guanine nucleotide-binding (G) domain / Dynamin-type guanine nucleotide-binding (G) domain profile. / Dynamin, N-terminal / Dynamin family / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / EH domain-containing protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.7 Å
AuthorsVazquez-Sarandeses, E. / Mikirtumov, V. / Noel, J. / Kudryashev, M. / Daumke, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
Citation
Journal: Nat Commun / Year: 2026
Title: Structures of EHD2 filaments on curved membranes provide a model for caveolar neck stabilization.
Authors: Elena Vázquez-Sarandeses / Vasilii Mikirtumov / Jeffrey K Noel / Mikhail Kudryashev / Oliver Daumke /
Abstract: 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 ...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.
#1: Journal: biorxiv.org / Year: 2025
Title: Structures of EHD2 filaments on curved membranes provides a model for caveolar neck stabilization
Authors: Vazquez-Sarandeses, E. / Mikirtumov, V. / Noel, J. / Kudryashev, M. / Daumke, O.
History
DepositionMay 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.1Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EH domain-containing protein 2
B: EH domain-containing protein 2
C: EH domain-containing protein 2
D: EH domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,23612
Polymers245,1104
Non-polymers2,1268
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Assembly is a row of dimers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
EH domain-containing protein 2


Mass: 61277.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Expressed in E. coli (BL21(DE3)-Rosetta2 strain) from a modified pET28 vector as N-terminal His6-tag fusions followed by a PreScission protease cleavage site.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ehd2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Rosetta2 / References: UniProt: Q8BH64
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: EHD2 with ATP and liposomes / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 20 mM HEPES/NaOH pH 7.5, 300 mM NaCl, 0.5 mM MgCl2
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 298 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Calibrated magnification: 42000 X / Nominal defocus max: 7000 nm / Nominal defocus min: 2000 nm / Calibrated defocus min: 2000 nm / Calibrated defocus max: 7000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2 e/Å2 / Avg electron dose per subtomogram: 100 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 1
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1Dynamovolume selection
2SerialEMimage acquisition
4GctfCTF correction
5RELION4CTF correction
11RELION4final Euler assignment
12cryoSPARCfinal Euler assignment
14RELION43D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75439 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: supersampling filament surface / Num. of tomograms: 61 / Num. of volumes extracted: 14491 / Reference model: not applicable
Atomic model buildingProtocol: FLEXIBLE FIT / Details: MDfit (Whitford et al., 2011)
Atomic model buildingPDB-ID: 4cid

4cid


Accession code: 4cid / Source name: PDB / Type: experimental model

+
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