5MTV

Active structure of EHD4 complexed with ATP-gamma-S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into the activation mechanism of dynamin-like EHD ATPases.

Melo, A.A.Hegde, B.G.Shah, C.Larsson, E.Isas, J.M.Kunz, S.Lundmark, R.Langen, R.Daumke, O.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 5629-5634

  • DOI: 10.1073/pnas.1614075114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Eps15 (epidermal growth factor receptor pathway substrate 15)-homology domain containing proteins (EHDs) comprise a family of dynamin-related mechano-chemical ATPases involved in cellular membrane trafficking. Previous studies have revealed the struc ...

    Eps15 (epidermal growth factor receptor pathway substrate 15)-homology domain containing proteins (EHDs) comprise a family of dynamin-related mechano-chemical ATPases involved in cellular membrane trafficking. Previous studies have revealed the structure of the EHD2 dimer, but the molecular mechanisms of membrane recruitment and assembly have remained obscure. Here, we determined the crystal structure of an amino-terminally truncated EHD4 dimer. Compared with the EHD2 structure, the helical domains are 50° rotated relative to the GTPase domain. Using electron paramagnetic spin resonance (EPR), we show that this rotation aligns the two membrane-binding regions in the helical domain toward the lipid bilayer, allowing membrane interaction. A loop rearrangement in GTPase domain creates a new interface for oligomer formation. Our results suggest that the EHD4 structure represents the active EHD conformation, whereas the EHD2 structure is autoinhibited, and reveal a complex series of domain rearrangements accompanying activation. A comparison with other peripheral membrane proteins elucidates common and specific features of this activation mechanism.


    Organizational Affiliation

    Crystallography Department, Max-Delbrück-Centrum for Molecular Medicine, 13125 Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EH domain-containing protein 4
A
523Mus musculusMutation(s): 0 
Gene Names: Ehd4 (Past2)
Find proteins for Q9EQP2 (Mus musculus)
Go to UniProtKB:  Q9EQP2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
A
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.227 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 199.973α = 90.00
b = 199.973β = 90.00
c = 41.537γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-10 
  • Released Date: 2017-03-08 
  • Deposition Author(s): Melo, A.A., Daumke, O.

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB958/A12

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-06-07
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence