3ATD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 10.1074/jbc.M111.278531
  • Primary Citation of Related Structures:  
    3ATA, 3ATB, 3ATD, 3ATE, 3AT8, 3AT9, 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 a ...

    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, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan. inanobe@pharma2.med.osaka-u.ac.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Potassium inwardly-rectifying channel, subfamily J, member 6A208Mus musculusMutation(s): 0 
Gene Names: Kcnj6
Find proteins for P48542 (Mus musculus)
Explore P48542 
Go to UniProtKB:  P48542
NIH Common Fund Data Resources
IMPC  MGI:104781
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GD
Query on GD

Download Ideal Coordinates CCD File 
A
GADOLINIUM ATOM
Gd
UIWYJDYFSGRHKR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.256 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.373α = 90
b = 82.373β = 90
c = 172.81γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: 2017-10-11
    Changes: Refinement description