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 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.250 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.4 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 (Paramagnetospirillum magnetotacticum)
Explore D9N164 
Go to UniProtKB:  D9N164
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9N164
Sequence Annotations
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  • 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 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.250 (Depositor) 
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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DDQClick on this verticalbar to view details

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
  • Version 1.4: 2024-10-16
    Changes: Structure summary