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

Validation slider image for 9RBU

This is version 1.0 of the entry. See complete history.

Literature

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

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

(2025) Biorxiv Org

DOI: https://doi.org/10.1101/2025.06.05.658037

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

Find similar proteins by:

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 G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D] 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 H [auth B] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] 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]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-08

Deposition Author(s):

Vazquez-Sarandeses, E.

Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History (Full details and data files)

Version 1.0: 2026-07-08
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.