9CZO | pdb_00009czo

Ca2+ bound intermediate state of hSlo1 + beta2N-beta4 channel in nanodisc.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Ball-and-chain inactivation of a human large conductance calcium-activated potassium channel.

Agarwal, S.Kim, E.D.Lee, S.Simon, A.Accardi, A.Nimigean, C.M.

(2025) Nat Commun 16: 1769-1769

  • DOI: https://doi.org/10.1038/s41467-025-56844-4
  • Primary Citation of Related Structures:  
    9CZH, 9CZJ, 9CZK, 9CZM, 9CZO, 9CZQ, 9D18, 9D19

  • PubMed Abstract: 

    BK channels are large-conductance calcium (Ca 2+ )-activated potassium channels crucial for neuronal excitability, muscle contraction, and neurotransmitter release. The pore-forming (α) subunits co-assemble with auxiliary (β and γ) subunits that modulate their function. Previous studies demonstrated that the N-termini of β2-subunits can inactivate BK channels, but with no structural correlate. Here, we investigate BK β2-subunit inactivation using cryo-electron microscopy, electrophysiology and molecular dynamics simulations. We find that the β2 N-terminus occludes the pore only in the Ca 2+ -bound open state, via a ball-and-chain mechanism. The first three hydrophobic residues of β2 are crucial for occlusion, while the remainder of the N-terminus remains flexible. Neither the closed channel conformation obtained in the absence of Ca 2+ nor an intermediate conformation found in the presence of Ca 2+ show density for the N-terminus of the β2 subunit in their pore, likely due to narrower side access portals preventing their entry into the channel pore.


  • Organizational Affiliation

    Department of Anesthesiology, Weill Cornell Medical College, 1300 York Ave, New York, NY, USA.


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-1
A, B, C, D
1,056Homo sapiensMutation(s): 0 
Gene Names: KCNMA1KCNMASLO
Membrane Entity: Yes 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel subunit beta-4
E, F, G, H
239Homo sapiensMutation(s): 0 
Gene Names: KCNMB2KCNMB4
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W47 (Homo sapiens)
Explore Q86W47 
Go to UniProtKB:  Q86W47
PHAROS:  Q86W47
GTEx:  ENSG00000135643 
Find proteins for B5BNX0 (Homo sapiens)
Explore B5BNX0 
Go to UniProtKB:  B5BNX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsB5BNX0Q86W47
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth D]
EA [auth D]
O [auth A]
P [auth A]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
I [auth A]
J [auth A]
S [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K (Subject of Investigation/LOI)
Query on K

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1
RECONSTRUCTIONRELION4.0.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release