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- PDB-9rc1: Cryo-ET structure of N-terminally truncated membrane-bound EHD2 c... -

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Basic information

Entry
Database: PDB / ID: 9rc1
TitleCryo-ET structure of N-terminally truncated 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 / deltaN / N-terminally truncated
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 / cilium assembly / endocytic vesicle / 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 / cilium assembly / endocytic vesicle / protein localization to plasma membrane / caveola / recycling endosome membrane / endocytosis / protein-macromolecule adaptor activity / early endosome / protein domain specific binding / hydrolase activity / calcium ion binding / GTP binding / perinuclear region of cytoplasm / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm / cytosol
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: 10.1 Å
AuthorsVazquez-Sarandeses, E. / Mikirtumov, V. / Noel, J. / Kudryashev, M. / Daumke, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)239,09012
Polymers236,9644
Non-polymers2,1268
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, flexible helical assembly on the tubes
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
EH domain-containing protein 2


Mass: 59240.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminally truncated (deleted residues 1-18)) / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ehd2 / Production host: Escherichia coli (E. coli) / 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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: N-terminally truncated 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

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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: 4 e/Å2 / Avg electron dose per subtomogram: 158 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

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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: 10.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17204 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionMethod: supersampling filament surface / Num. of tomograms: 100 / Num. of volumes extracted: 30449 / 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

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