9CZK | pdb_00009czk

Ca2+ free hSlo1 + beta2N-beta4 channel in nanodisc.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9CZK

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 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.

Macromolecule Content 

  • Total Structure Weight: 590.27 kDa 
  • Atom Count: 35,075 
  • Modeled Residue Count: 4,396 
  • Deposited Residue Count: 5,180 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  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:|  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 B5BNX0 (Homo sapiens)
Explore B5BNX0 
Go to UniProtKB:  B5BNX0
Find proteins for Q86W47 (Homo sapiens)
Explore Q86W47 
Go to UniProtKB:  Q86W47
PHAROS:  Q86W47
GTEx:  ENSG00000135643 
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
K [auth A],
M [auth B],
Q [auth F],
R [auth G]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR
(Subject of Investigation/LOI)

Query on CLR



Download:Ideal Coordinates CCD File
L [auth A],
N [auth B],
O [auth C],
P [auth D]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
K
(Subject of Investigation/LOI)

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: 3.50 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