9OA8 | pdb_00009oa8

Cryo-EM structure of KCa3.1/calmodulin channel in complex with NS309


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for the subtype-selectivity of K Ca 2.2 channel activators.

Zhang, M.Nam, Y.W.Ramanishka, A.Xu, Y.Yasuda, R.M.Im, D.Cui, M.Chandy, G.Wulff, H.

(2025) Res Sq 

  • DOI: https://doi.org/10.21203/rs.3.rs-6568445/v1
  • Primary Citation of Related Structures:  
    9O7S, 9O85, 9O93, 9OA8

  • PubMed Abstract: 

    Small-conductance (K Ca 2.2) and intermediate-conductance (K Ca 3.1) Ca 2+ -activated K + channels are gated by a Ca 2+ -calmodulin dependent mechanism. NS309 potentiates the activity of both K Ca 2.2 and K Ca 3.1, while rimtuzalcap selectively activates K Ca 2.2. Rimtuzalcap has been used in clinical trials for the treatment of spinocerebellar ataxia and essential tremor. We report cryo-electron microscopy structures of K Ca 2.2 channels bound with NS309 and rimtuzalcap, in addition to K Ca 3.1 channels with NS309. The different conformations of calmodulin and the cytoplasmic HC helices in the two channels underlie the subtype-selectivity of rimtuzalcap for K Ca 2.2. Calmodulin's N-lobes in the K Ca 2.2 structure are far apart and undergo conformational changes to accommodate either NS309 or rimtuzalcap. Calmodulin's Nlobes in the K Ca 3.1 structure are closer to each other and are constrained by the HC helices of K Ca 3.1, which allows binding of NS309 but not of the bulkier rimtuzalcap. These structures provide a framework for structure-based drug design targeting K Ca 2.2 channels.


  • Organizational Affiliation
    • Chapman University.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Intermediate conductance calcium-activated potassium channel protein 4
A, B, C, D
378Homo sapiensMutation(s): 0 
Gene Names: KCNN4IK1IKCA1KCA4SK4
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15554
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
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1KP (Subject of Investigation/LOI)
Query on 1KP

Download Ideal Coordinates CCD File 
L [auth E],
O [auth F],
R [auth G],
U [auth H]
(3E)-6,7-dichloro-3-(hydroxyimino)-1,3-dihydro-2H-indol-2-one
C8 H4 Cl2 N2 O2
CVOUSAVHMDXCKG-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
M [auth E]
N [auth E]
P [auth F]
Q [auth F]
S [auth G]
M [auth E],
N [auth E],
P [auth F],
Q [auth F],
S [auth G],
T [auth G],
V [auth H],
W [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]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States23AIREA1039423
American Heart AssociationUnited States24CDA1260237
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United States4R33 NS101182-03
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR15 NS130420-01A1

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2025-06-25
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-17
    Changes: Data collection, Structure summary
  • Version 2.0: 2025-10-01
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description