8V2H | pdb_00008v2h

Cryo-EM structure of the KCa2.2 channel bound to inhibitor AP14145.


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 1.2 of the entry. See complete history


Literature

Cryo-EM structures of the small-conductance Ca 2+ -activated K Ca 2.2 channel.

Nam, Y.W.Im, D.Garcia, A.S.C.Tringides, M.L.Nguyen, H.M.Liu, Y.Orfali, R.Ramanishka, A.Pintilie, G.Su, C.C.Cui, M.Logothetis, D.E.Yu, E.W.Wulff, H.Chandy, K.G.Zhang, M.

(2025) Nat Commun 16: 3690-3690

  • DOI: https://doi.org/10.1038/s41467-025-59061-1
  • Primary Citation of Related Structures:  
    8V2G, 8V2H, 8V3G, 9EIO

  • PubMed Abstract: 

    Small-conductance Ca 2+ -activated K + (K Ca 2.1-K Ca 2.3) channels modulate neuronal and cardiac excitability. We report cryo-electron microscopy structures of the K Ca 2.2 channel in complex with calmodulin and Ca 2+ , alone or bound to two small molecule inhibitors, at 3.18, 3.50, 2.99 and 2.97 angstrom resolution, respectively. Extracellular S3-S4 loops in β-hairpin configuration form an outer canopy over the pore with an aromatic box at the canopy's center. Each S3-S4 β-hairpin is tethered to the selectivity filter in the neighboring subunit by inter-subunit hydrogen bonds. This hydrogen bond network flips the aromatic residue (Tyr362) in the filter's GYG signature by 180°, causing the outer selectivity filter to widen and water to enter the filter. Disruption of the tether by a mutation narrows the outer selectivity filter, realigns Tyr362 to the position seen in other K + channels, and significantly increases unitary conductance. UCL1684, a mimetic of the bee venom peptide apamin, sits atop the canopy and occludes the opening in the aromatic box. AP14145, an analogue of a therapeutic for atrial fibrillation, binds in the central cavity below the selectivity filter and induces closure of the inner gate. These structures provide a basis for understanding the small unitary conductance and pharmacology of K Ca 2.x channels.


  • Organizational Affiliation
    • Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, 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,
C [auth B],
E [auth C],
G [auth D]
361Rattus norvegicusMutation(s): 0 
Gene Names: Kcnn2
Membrane Entity: Yes 
UniProt
Find proteins for P70604 (Rattus norvegicus)
Explore P70604 
Go to UniProtKB:  P70604
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70604
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin-1B [auth E],
D [auth F],
F [auth G],
H
146Rattus norvegicusMutation(s): 0 
Gene Names: Calm1CalmCamCam1CaMI
UniProt
Find proteins for P0DP29 (Rattus norvegicus)
Explore P0DP29 
Go to UniProtKB:  P0DP29
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP29
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
M [auth E]
N [auth E]
O [auth F]
P [auth F]
Q [auth G]
M [auth E],
N [auth E],
O [auth F],
P [auth F],
Q [auth G],
R [auth G],
S [auth H],
T [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [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 REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States23AIREA1039423
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS101182-03

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-07
    Changes: Data collection