4CID | pdb_00004cid

Structural insights into the N-terminus of the EHD2 ATPase

• PDB DOI: https://doi.org/10.2210/pdb4CID/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-12-06 Released: 2014-02-19 
• Deposition Author(s): Shah, C., Daumke, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.279 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structural Insights Into Membrane Interaction and Caveolar Targeting of Dynamin-Like Ehd2.

Shah, C., Hegde, B.G., Mor, B., Behrmann, E., Mielke, T., Moenke, G., Spahn, C.M., Lundmark, R., Daumke, O., Langen, R.

(2014) Structure 22: 409

• PubMed: 24508342 
• DOI: https://doi.org/10.1016/j.str.2013.12.015
• Primary Citation Related Structures: 
  4CID


• PubMed Abstract: 
  

  The dynamin-related Eps15-homology domain-containing protein 2 (EHD2) is a membrane-remodeling ATPase that regulates the dynamics of caveolae. Here, we established an electron paramagnetic resonance (EPR) approach to characterize structural features of membrane-bound EHD2. We show that residues at the tip of the helical domain can insert into the membrane and may create membrane curvature by a wedging mechanism. Using EPR and X-ray crystallography, we found that the N terminus is folded into a hydrophobic pocket of the GTPase domain in solution and can be released into the membrane. Cryoelectron microscopy demonstrated that the N terminus is not essential for oligomerization of EHD2 into a membrane-anchored scaffold. Instead, we found a function of the N terminus in regulating targeting and stable association of EHD2 to caveolae. Our data uncover an unexpected, membrane-induced regulatory switch in EHD2 and demonstrate the versatility of EPR to study structure and function of dynamin superfamily proteins.

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Organizational Affiliation: 
• Max-Delbrück-Center for Molecular Medicine, Crystallography, Robert-Rössle-Straße 10, 13092 Berlin, Germany.
Institute of Chemistry and Biochemistry, Free University Berlin, Takustraße 6, 14195 Berlin, Germany.
Post Graduate Department of Physics, Rani Channamma University, Vidyasangama, Belagavi-591156, India.
Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden.
Institute of Medical Physics and Biophysics, Charité, Charitéplatz 1, 10117 Berlin, Germany.
UltraStrukturNetzwerk, Max-Planck-Institute for Molecular Genetics, Ihnestraße 73, 14195 Berlin.
Zilkha Neurogenetic Institute, University of Southern California, 1501 San Pablo Street, Los Angeles, CA 90033, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.21 kDa 
• Atom Count: 3,993 
• Modeled Residue Count: 497 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EH DOMAIN-CONTAINING PROTEIN 2	A	550	Mus musculus	Mutation(s): 2  EC: 3.6.5.5
UniProt
Find proteins for Q8BH64 (Mus musculus) Explore Q8BH64  Go to UniProtKB:  Q8BH64

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.279 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.851	α = 90
b = 134.653	β = 106.05
c = 56.068	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
SHARP	phasing
REFMAC	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Shah, C., Daumke, O.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2014-03-19
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary