SPFH domain of mouse stomatin (Crystal form 3)

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history


A stomatin dimer modulates the activity of acid-sensing ion channels.

Brand, J.Smith, E.S.Schwefel, D.Lapatsina, L.Poole, K.Omerbasic, D.Kozlenkov, A.Behlke, J.Lewin, G.R.Daumke, O.

(2012) EMBO J 31: 3635-3646

  • DOI: https://doi.org/10.1038/emboj.2012.203
  • Primary Citation of Related Structures:  
    4FVF, 4FVG, 4FVJ

  • PubMed Abstract: 

    Stomatin proteins oligomerize at membranes and have been implicated in ion channel regulation and membrane trafficking. To obtain mechanistic insights into their function, we determined three crystal structures of the conserved stomatin domain of mouse stomatin that assembles into a banana-shaped dimer. We show that dimerization is crucial for the repression of acid-sensing ion channel 3 (ASIC3) activity. A hydrophobic pocket at the inside of the concave surface is open in the presence of an internal peptide ligand and closes in the absence of this ligand, and we demonstrate a function of this pocket in the inhibition of ASIC3 activity. In one crystal form, stomatin assembles via two conserved surfaces into a cylindrical oligomer, and these oligomerization surfaces are also essential for the inhibition of ASIC3-mediated currents. The assembly mode of stomatin uncovered in this study might serve as a model to understand oligomerization processes of related membrane-remodelling proteins, such as flotillin and prohibitin.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Stomatin133Mus musculusMutation(s): 3 
Gene Names: Epb7.2Epb72Stom
Find proteins for P54116 (Mus musculus)
Explore P54116 
Go to UniProtKB:  P54116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54116
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.489α = 90
b = 84.489β = 90
c = 68.937γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description