Structure of aquaporin-4 S180D mutant at 2.8 A resolution by electron crystallography

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

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This is version 2.2 of the entry. See complete history


Mechanism of Aquaporin-4's Fast and Highly Selective Water Conduction and Proton Exclusion.

Tani, K.Mitsuma, T.Hiroaki, Y.Kamegawa, A.Nishikawa, K.Tanimura, Y.Fujiyoshi, Y.

(2009) J Mol Biol 389: 694-706

  • DOI: https://doi.org/10.1016/j.jmb.2009.04.049
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Members of the aquaporin (AQP) family are expressed in almost every organism, including 13 homologues in humans. Based on the electron crystallographic structure of AQP1, the hydrogen-bond isolation mechanism was proposed to explain why AQPs are impermeable to protons despite their very fast water conduction. The mechanism by which AQPs exclude protons remained controversial, however. Here we present the structure of AQP4 at 2.8 A resolution obtained by electron crystallography of double-layered two-dimensional crystals. The resolution has been improved from the previous 3.2 A, with accompanying improvement in data quality resulting in the ability to identify individual water molecules. Our structure of AQP4, the predominant water channel in the brain, reveals eight water molecules in the channel. The arrangement of the waters provides support for the hydrogen-bond isolation mechanism. Our AQP4 structure also visualizes five lipids, showing that direct interactions of the extracellular surface of AQP4 with three lipids in the adjoining membrane help stabilize the membrane junction.

  • Organizational Affiliation

    Department of Biophysics, Faculty of Science, Kyoto University, Oiwake, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aquaporin-4301Rattus norvegicusMutation(s): 1 
Gene Names: Aqp4
Membrane Entity: Yes 
Find proteins for P47863 (Rattus norvegicus)
Explore P47863 
Go to UniProtKB:  P47863
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47863
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69α = 90
b = 69β = 90
c = 160γ = 90
Software Package:
Software NamePurpose
MRCdata collection
MRCdata reduction
MRCdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-10-29
    Changes: Non-polymer description
  • Version 2.0: 2021-11-10
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection
  • Version 2.2: 2023-11-08
    Changes: Refinement description