Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 35.94 kDa 
• Atom Count: 1867 
• Modelled Residue Count: 223 
• Deposited Residue Count: 301 
• Unique protein chains: 1

2ZZ9

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

• PDB DOI: 10.2210/pdb2ZZ9/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMMemProtMDmpstruc


• Deposited: 2009-02-06 Released: 2009-06-09 
• Deposition Author(s): Tani, K., Mitsuma, T., Hiroaki, Y., Kamegawa, A., Nishikawa, K., Tanimura, Y., Fujiyoshi, Y.

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Experimental Data Snapshot

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

Literature

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

• PubMed: 19406128 
• DOI: 10.1016/j.jmb.2009.04.049
• Primary Citation of Related Structures:  
  2ZZ9


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aquaporin-4	A	301	Rattus norvegicus	Mutation(s): 1  Gene Names: Aqp4 Membrane Entity: Yes
UniProt
Find proteins for P47863 (Rattus norvegicus) Explore P47863  Go to UniProtKB:  P47863

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEE	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine C41 H78 N O8 P MWRBNPKJOOWZPW-NYVOMTAGSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• 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 = 69	α = 90
b = 69	β = 90
c = 160	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MRC	data collection
MRC	data reduction
MRC	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-02-06 
• Released Date: 2009-06-09 
Deposition Author(s): Tani, K., Mitsuma, T., Hiroaki, Y., Kamegawa, A., Nishikawa, K., Tanimura, Y., Fujiyoshi, Y.

Revision History  

• 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