6O9U | pdb_00006o9u

KirBac3.1 at a resolution of 2 Angstroms

• PDB DOI: https://doi.org/10.2210/pdb6O9U/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Paramagnetospirillum magnetotacticum
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2019-03-15 Released: 2020-05-27 
• Deposition Author(s): Gulbis, J.M., Clarke, O.B.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.202 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

A constricted opening in Kir channels does not impede potassium conduction.

Black, K.A., He, S., Jin, R., Miller, D.M., Bolla, J.R., Clarke, O.B., Johnson, P., Windley, M., Burns, C.J., Hill, A.P., Laver, D., Robinson, C.V., Smith, B.J., Gulbis, J.M.

(2020) Nat Commun 11: 3024-3024

• PubMed: 32541684 
• DOI: https://doi.org/10.1038/s41467-020-16842-0
• Primary Citation Related Structures: 
  6O9T, 6O9U, 6O9V


• PubMed Abstract: 
  

  The canonical mechanistic model explaining potassium channel gating is of a conformational change that alternately dilates and constricts a collar-like intracellular entrance to the pore. It is based on the premise that K ⁺ ions maintain a complete hydration shell while passing between the transmembrane cavity and cytosol, which must be accommodated. To put the canonical model to the test, we locked the conformation of a Kir K ⁺ channel to prevent widening of the narrow collar. Unexpectedly, conduction was unimpaired in the locked channels. In parallel, we employed all-atom molecular dynamics to simulate K ⁺ ions moving along the conduction pathway between the lower cavity and cytosol. During simulations, the constriction did not significantly widen. Instead, transient loss of some water molecules facilitated K ⁺ permeation through the collar. The low free energy barrier to partial dehydration in the absence of conformational change indicates Kir channels are not gated by the canonical mechanism.

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Organizational Affiliation: 
• Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia.
La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, OX1 3QZ, UK.
Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
School of Biomedical Sciences and Pharmacy, The University of Newcastle, Newcastle, NSW, 2300, Australia.
Computational Cardiology Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.
Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia. [e-mail].
Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. [e-mail].
Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 36.37 kDa 
• Atom Count: 2,473 
• Modeled Residue Count: 283 
• Deposited Residue Count: 301 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inward rectifier potassium channel Kirbac3.1	A	301	Paramagnetospirillum magnetotacticum	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for D9N164 (Paramagnetospirillum magnetotacticum) Explore D9N164  Go to UniProtKB:  D9N164

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCW	P [auth A], Q [auth A]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
Z3P	R [auth A]	3,3',3''-phosphoryltripropanoic acid C9 H15 O7 P XJGZCDJZBUBTKW-UHFFFAOYSA-N
BA	N [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
TMO	B [auth A], C [auth A], D [auth A]	trimethylamine oxide C3 H9 N O UYPYRKYUKCHHIB-UHFFFAOYSA-N
K	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.202 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.955	α = 90
b = 105.955	β = 90
c = 89.639	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Gulbis, J.M., Clarke, O.B.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2020-12-09
  Changes: Database references, Derived calculations
• Version 1.2: 2020-12-16
  Changes: Database references
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description