3ATF

Crystal Structure of the Kir3.2 Cytoplasmic Domain (Na+-free crystal soaked in 200 mM Cesium chloride)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Potassium inwardly-rectifying channel, subfamily J, member 6
A
208Mus musculusMutation(s): 0 
Gene Names: Kcnj6 (Girk2, Kcnj7, W)
Find proteins for P48542 (Mus musculus)
Go to UniProtKB:  P48542
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
CS
Query on CS
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Download CCD File 
A
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH
Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.223 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 81.732α = 90.00
b = 81.732β = 90.00
c = 172.125γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2017-08-16
    Type: Refinement description, Source and taxonomy
  • Version 1.3: 2017-10-11
    Type: Refinement description