Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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: 24.17 kDa 
• Atom Count: 1576 
• Residue Count: 196 
• Unique protein chains: 1

3ATE

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

• DOI: 10.2210/pdb3ATE/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-28 Released: 2011-10-19 
• Deposition Author(s): Inanobe, A., Kurachi, Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.325 
• R-Value Work: 0.267 
• R-Value Observed: 0.274 

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

• PubMed: 21982822 
• 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 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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium inwardly-rectifying channel, subfamily J, member 6	A	208	Mus musculus	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PR	A	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.325 
• R-Value Work: 0.267 
• R-Value Observed: 0.274 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.775	α = 90
b = 82.775	β = 90
c = 172.894	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-12-28 
• Released Date: 2011-10-19 
Deposition Author(s): Inanobe, A., Kurachi, Y.

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: Advisory, Refinement description, Source and taxonomy
• Version 1.3: 2017-10-11
  Changes: Refinement description