6ALE

A V-to-F substitution in SK2 channels causes Ca2+ hypersensitivity and improves locomotion in a C. elegans ALS model


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A V-to-F substitution in SK2 channels causes Ca2+hypersensitivity and improves locomotion in a C. elegans ALS model.

Nam, Y.W.Baskoylu, S.N.Gazgalis, D.Orfali, R.Cui, M.Hart, A.C.Zhang, M.

(2018) Sci Rep 8: 10749-10749

  • DOI: https://doi.org/10.1038/s41598-018-28783-2
  • Primary Citation of Related Structures:  
    6ALE, 6CZQ

  • PubMed Abstract: 

    Small-conductance Ca 2+ -activated K + (SK) channels mediate medium afterhyperpolarization in the neurons and play a key role in the regulation of neuronal excitability. SK channels are potential drug targets for ataxia and Amyotrophic Lateral Sclerosis (ALS). SK channels are activated exclusively by the Ca 2+ -bound calmodulin. Previously, we identified an intrinsically disordered fragment that is essential for the mechanical coupling between Ca 2+ /calmodulin binding and channel opening. Here, we report that substitution of a valine to phenylalanine (V407F) in the intrinsically disordered fragment caused a ~6 fold increase in the Ca 2+ sensitivity of SK2-a channels. This substitution resulted in a novel interaction between the ectopic phenylalanine and M411, which stabilized PIP 2 -interacting residue K405, and subsequently enhanced Ca 2+ sensitivity. Also, equivalent valine to phenylalanine substitutions in SK1 or SK3 channels conferred Ca 2+ hypersensitivity. An equivalent phenylalanine substitution in the Caenorhabditis elegans (C. elegans) SK2 ortholog kcnl-2 partially rescued locomotion defects in an existing C. elegans ALS model, in which human SOD1G85R is expressed at high levels in neurons, confirming that this phenylalanine substitution impacts channel function in vivo. This work for the first time provides a critical reagent for future studies: an SK channel that is hypersensitive to Ca 2+ with increased activity in vivo.


  • Organizational Affiliation

    Department of Biomedical and Pharmaceutical Sciences & Structural Biology Research Center, Chapman University School of Pharmacy, Irvine, California, 92618, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Small conductance calcium-activated potassium channel protein 2A [auth B]95Homo sapiensMutation(s): 0 
Gene Names: KCNN2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2S1 (Homo sapiens)
Explore Q9H2S1 
Go to UniProtKB:  Q9H2S1
PHAROS:  Q9H2S1
GTEx:  ENSG00000080709 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2S1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-2B [auth R]146Rattus norvegicusMutation(s): 0 
Gene Names: Calm2Cam2CambCaMII
UniProt
Find proteins for P0DP30 (Rattus norvegicus)
Explore P0DP30 
Go to UniProtKB:  P0DP30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP30
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1KP
Query on 1KP

Download Ideal Coordinates CCD File 
F [auth B](3E)-6,7-dichloro-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-one
C8 H4 Cl2 N2 O2
CVOUSAVHMDXCKG-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B],
E [auth B],
J [auth R]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth R],
I [auth R]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.653α = 90
b = 66.913β = 92.47
c = 64.712γ = 90
Software Package:
Software NamePurpose
XPREPdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XPREPdata reduction
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States13SDG16150007
National Ataxia FoundationUnited StatesYI-SCA

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references