10AD | pdb_000010ad

Cryo-EM structure of the human BK channel bound to the agonist NS1619


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The BK channel-NS1619 agonist complex reveals molecular insights into allosteric activation gating.

Gonzalez-Sanabria, N.Contreras, G.F.Rojas, M.Duarte, Y.Gonzalez-Nilo, F.D.Perozo, E.Latorre, R.

(2026) Proc Natl Acad Sci U S A 123: e2507707123-e2507707123

  • DOI: https://doi.org/10.1073/pnas.2507707123
  • Primary Citation of Related Structures:  
    10AD

  • PubMed Abstract: 

    BK channels play essential roles in a wealth of physiological functions, including regulating smooth muscle tone and neurotransmitter release. Its dysfunction, often caused by loss-of-function mutations, can lead to severe phenotypes, including ataxia and sensory impairment. Despite the therapeutic potential of BK channel agonists, the molecular mechanisms by which they stabilize the pore's open conformation remain unclear. Using cryoelectron microscopy and molecular dynamic simulations, we identified that NS1619, a synthetic benzimidazolone agonist, first described as a BK opener, binds within a pocket formed by the S6/RCK1 linker and the S4 transmembrane segment. Our simulations suggest that agonist binding promotes a twisting motion in the S6 segment, enabling critical interactions with residues K330, K331, and F223. These findings provide a molecular model for the mechanism of NS1619 and suggest that its binding site can accommodate other agonists, highlighting a promising target for therapeutic development.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 5 of Calcium-activated potassium channel subunit alpha-1A [auth E],
B [auth C],
C [auth D],
D [auth A]
1,113Homo sapiensMutation(s): 0 
Gene Names: KCNMA1KCNMASLO
UniProt & NIH Common Fund Data Resources
Find proteins for Q12791 (Homo sapiens)
Explore Q12791 
Go to UniProtKB:  Q12791
PHAROS:  Q12791
GTEx:  ENSG00000156113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12791
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1E02 (Subject of Investigation/LOI)
Query on A1E02

Download Ideal Coordinates CCD File 
H [auth E],
L [auth C],
P [auth D],
T [auth A]
3-[2-oxidanyl-5-(trifluoromethyl)phenyl]-6-(trifluoromethyl)-1~{H}-benzimidazol-2-one
C15 H8 F6 N2 O2
YLFMCMWKHSDUCT-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth E]
G [auth E]
J [auth C]
K [auth C]
N [auth D]
F [auth E],
G [auth E],
J [auth C],
K [auth C],
N [auth D],
O [auth D],
R [auth A],
S [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E,
I [auth C],
M [auth D],
Q [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONCoot
MODEL REFINEMENTPHENIX1.21.2_5419

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1230265
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM150272
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM030376
Agencia Nacional de Investigación y Desarrollo (ANID)Chile21200592

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-04
    Type: Initial release
  • Version 1.1: 2026-02-11
    Changes: Data collection, Database references