9O48 | pdb_00009o48

Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex in the Ca2+ bound state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of SK2 channel gating and its modulation by the bee toxin apamin and small molecules.

Cassell, S.J.Li, W.Krautwald, S.Khoshouei, M.Lee, Y.T.Hou, J.Guan, W.Peukert, S.Weihofen, W.Whicher, J.R.

(2025) Elife 14

  • DOI: https://doi.org/10.7554/eLife.107733
  • Primary Citation of Related Structures:  
    9O48, 9O51, 9O52, 9O53, 9O5O

  • PubMed Abstract: 

    Small-conductance calcium-activated potassium channel 2 (SK2) serves a variety of biological functions by coupling intracellular calcium dynamics with membrane potential. SK2 modulators are in development for the treatment of neurological and cardiovascular diseases, though the mechanisms of pharmacological modulation remain incompletely understood. We determined structures of an SK2-4 chimeric channel in Ca 2+ -bound and Ca 2+ -free conformations and in complex with the bee toxin apamin, a small molecule inhibitor, and a small molecule activator. The structures revealed that the S3-S4 linker forms a hydrophobic constriction at the extracellular opening of the pore. Apamin binds to this extracellular constriction and blocks the exit of potassium ions. Furthermore, we identified a structurally related SK2 inhibitor and activator that bind to the transmembrane domains. The compounds exert opposing effects on gating by differentially modulating the conformation of the S6 helices. These results provide important mechanistic insights to facilitate the development of targeted SK2 channel therapeutics.


  • Organizational Affiliation
    • Discovery Sciences, Novartis Biomedical Research, Cambridge, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intermediate conductance calcium-activated potassium channel protein 4,Small conductance calcium-activated potassium channel protein 2 chimera
A, B, C, D
435Homo sapiensMutation(s): 0 
Gene Names: KCNN4IK1IKCA1KCA4SK4KCNN2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for O15554 (Homo sapiens)
Explore O15554 
Go to UniProtKB:  O15554
PHAROS:  O15554
GTEx:  ENSG00000104783 
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 GroupsO15554Q9H2S1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1
E, F, G, H
149Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth E]
L [auth E]
M [auth E]
N [auth E]
O [auth F]
K [auth E],
L [auth E],
M [auth E],
N [auth E],
O [auth F],
P [auth F],
Q [auth F],
R [auth F],
S [auth G],
T [auth G],
U [auth G],
V [auth G],
W [auth H],
X [auth H],
Y [auth H],
Z [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Data collection, Database references