6O9V

KirBac3.1 mutant at a resolution of 3.1 Angstroms


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-020-16842-0
  • Primary Citation of 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.


  • Organizational Affiliation

    Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inward rectifier potassium channel Kirbac3.1
A, B
301Paramagnetospirillum magnetotacticumMutation(s): 5 
Membrane Entity: Yes 
UniProt
Find proteins for D9N164 (Magnetospirillum magnetotacticum)
Explore D9N164 
Go to UniProtKB:  D9N164
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9N164
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M1M
Query on M1M

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
1,1-Methanediyl Bismethanethiosulfonate
C3 H8 O4 S4
SFSDVHMSSISWGL-UHFFFAOYSA-N
DDQ
Query on DDQ

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
DECYLAMINE-N,N-DIMETHYL-N-OXIDE
C12 H27 N O
ZRKZFNZPJKEWPC-UHFFFAOYSA-N
TMO
Query on TMO

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.298α = 90
b = 114.683β = 90
c = 89.457γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • 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