Crystal Structure of the Kir3.2 Cytoplasmic Domain (Na+-free crystal soaked in 10 mM barium chloride)

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.247 

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Interactions of cations with the cytoplasmic pores of inward rectifier K(+) channels in the closed state

Inanobe, A.Nakagawa, A.Kurachi, Y.

(2011) J Biol Chem 286: 41801-41811

  • DOI: https://doi.org/10.1074/jbc.M111.278531
  • Primary Citation of Related Structures:  
    3AT8, 3AT9, 3ATA, 3ATB, 3ATD, 3ATE, 3ATF

  • PubMed Abstract: 

    Ion channels gate at membrane-embedded domains by changing their conformation along the ion conduction pathway. Inward rectifier K(+) (Kir) channels possess a unique extramembrane cytoplasmic domain that extends this pathway. However, the relevance and contribution of this domain to ion permeation remain unclear. By qualitative x-ray crystallographic analysis, we found that the pore in the cytoplasmic domain of Kir3.2 binds cations in a valency-dependent manner and does not allow the displacement of Mg(2+) by monovalent cations or spermine. Electrophysiological analyses revealed that the cytoplasmic pore of Kir3.2 selectively binds positively charged molecules and has a higher affinity for Mg(2+) when it has a low probability of being open. The selective blocking of chemical modification of the side chain of pore-facing residues by Mg(2+) indicates that the mode of binding of Mg(2+) is likely to be similar to that observed in the crystal structure. These results indicate that the Kir3.2 crystal structure has a closed conformation with a negative electrostatic field potential at the cytoplasmic pore, the potential of which may be controlled by conformational changes in the cytoplasmic domain to regulate ion diffusion along the pore.

  • Organizational Affiliation

    Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan; Center for Advanced Medical Engineering and Informatics, Osaka University, Osaka 565-0871, Japan. Electronic address: inanobe@pharma2.med.osaka-u.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Potassium inwardly-rectifying channel, subfamily J, member 6208Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P48542 (Mus musculus)
Explore P48542 
Go to UniProtKB:  P48542
IMPC:  MGI:104781
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48542
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on BA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.247 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.833α = 90
b = 81.833β = 90
c = 172.463γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references