Voltage-gated proton channel: VSOP/Hv1 chimeric channel

Experimental Data Snapshot

  • Resolution: 3.45 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.341 
  • R-Value Observed: 0.342 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


X-ray crystal structure of voltage-gated proton channel.

Takeshita, K.Sakata, S.Yamashita, E.Fujiwara, Y.Kawanabe, A.Kurokawa, T.Okochi, Y.Matsuda, M.Narita, H.Okamura, Y.Nakagawa, A.

(2014) Nat Struct Mol Biol 21: 352-357

  • DOI: https://doi.org/10.1038/nsmb.2783
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The voltage-gated proton channel Hv1 (or VSOP) has a voltage-sensor domain (VSD) with dual roles of voltage sensing and proton permeation. Its gating is sensitive to pH and Zn(2+). Here we present a crystal structure of mouse Hv1 in the resting state at 3.45-Å resolution. The structure showed a 'closed umbrella' shape with a long helix consisting of the cytoplasmic coiled coil and the voltage-sensing helix, S4, and featured a wide inner-accessible vestibule. Two out of three arginines in S4 were located below the phenylalanine constituting the gating charge-transfer center. The extracellular region of each protomer coordinated a Zn(2+), thus suggesting that Zn(2+) stabilizes the resting state of Hv1 by competing for acidic residues that otherwise form salt bridges with voltage-sensing positive charges on S4. These findings provide a platform for understanding the general principles of voltage sensing and proton permeation.

  • Organizational Affiliation

    1] Institute for Protein Research, Osaka University, Suita, Japan. [2] Graduate School of Medicine, Osaka University, Suita, Japan. [3] Institute for Academic Initiatives, Osaka University, Suita, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ion channel196Mus musculusMutation(s): 0 
Membrane Entity: Yes 
Find proteins for Q3U2S8 (Mus musculus)
Explore Q3U2S8 
Go to UniProtKB:  Q3U2S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3U2S8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.45 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.341 
  • R-Value Observed: 0.342 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.54α = 90
b = 86.54β = 90
c = 89.553γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
BSSdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references