9RBU | pdb_00009rbu

Cryo-ET structure of full-length membrane-bound EHD2 complex

PDB DOI: https://doi.org/10.2210/pdb9RBU/pdb
EM Map EMD-53909: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-27 Released: 2026-07-08
Deposition Author(s): Vazquez-Sarandeses, E., Mikirtumov, V., Noel, J., Kudryashev, M., Daumke, O.
Funding Organization(s): Helmholtz Association

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.70 Å
Aggregation State: FILAMENT
Reconstruction Method: SUBTOMOGRAM AVERAGING

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structures of EHD2 filaments on curved membranes provide a model for caveolar neck stabilization.

Vazquez-Sarandeses, E., Mikirtumov, V., Noel, J.K., Kudryashev, M., Daumke, O.

(2026) Nat Commun 17

PubMed: 42538327 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-76288-8
Primary Citation Related Structures:
9RBU, 9RC1

PubMed 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 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.

Organizational Affiliation

Structural Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 247.24 kDa
Atom Count: 16,024
Modeled Residue Count: 2,028
Deposited Residue Count: 2,172
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EH domain-containing protein 2	A, B, C, D	543	Mus musculus	Mutation(s): 0 Gene Names: Ehd2
UniProt
Find proteins for Q8BH64 (Mus musculus) Explore Q8BH64 Go to UniProtKB: Q8BH64
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8BH64
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]