3AUW

Cytoplasmic domain of inward rectifier potassium channel Kir3.2 in complex with cadmium

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Inverse agonist-like action of cadmium on G-protein-gated inward-rectifier K(+) channels

Inanobe, A., Matsuura, T., Nakagawa, A., Kurachi, Y.

(2011) Biochem.Biophys.Res.Commun. 407: 366-371

  • DOI: 10.1016/j.bbrc.2011.03.025

  • PubMed Abstract: 

    • The gate at the pore-forming domain of potassium channels is allosterically controlled by a stimulus-sensing domain. Using Cd²(+) as a probe, we examined the structural elements responsible for gating in an inward-rectifier K(+) channel (Kir3.2). One ...

    The gate at the pore-forming domain of potassium channels is allosterically controlled by a stimulus-sensing domain. Using Cd²(+) as a probe, we examined the structural elements responsible for gating in an inward-rectifier K(+) channel (Kir3.2). One of four endogenous cysteines facing the cytoplasm contributes to a high-affinity site for inhibition by internal Cd²(+). Crystal structure of its cytoplasmic domain in complex with Cd²(+) reveals that octahedral coordination geometry supports the high-affinity binding. This mode of action causes the tethering of the N-terminus to CD loop in the stimulus-sensing domain, suggesting that their conformational changes participate in gating and Cd²(+) inhibits Kir3.2 by trapping the conformation in the closed state like "inverse agonist".

    Organizational Affiliation: 

    Department of Pharmacology, Graduate School of Medicine, Osaka University, Osaka, 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, C
26Mus musculusMutation(s): 0 
Gene Names: Kcnj6 (Girk2, Kcnj7, W)
Find proteins for P48542 (Mus musculus)
Go to UniProtKB:  P48542
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Potassium inwardly-rectifying channel, subfamily J, member 6
B, D
182Mus 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
Download SDF File 
Download CCD File 
B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH
Download SDF File 
Download CCD File 
B, D
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD
Download SDF File 
Download CCD File 
A, C
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.56 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.281 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.808α = 90.00
b = 100.808β = 90.00
c = 105.812γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Refinement description