9CZM | pdb_00009czm

Ca2+ bound open-inactivated hSlo1 + beta2N-beta4 channel in nanodisc.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 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
Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel subunit beta-4A [auth E],
B [auth F],
C [auth H],
H [auth G]
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 5 of Calcium-activated potassium channel subunit alpha-1D [auth A],
E [auth B],
F [auth C],
G [auth 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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AB [auth D]
CA [auth B]
DA [auth B]
EA [auth B]
EB [auth D]
AB [auth D],
CA [auth B],
DA [auth B],
EA [auth B],
EB [auth D],
FB [auth D],
GB [auth D],
HA [auth B],
I [auth A],
IA [auth B],
JA [auth B],
JB [auth D],
KA [auth B],
KB [auth D],
LA [auth B],
LB [auth D],
M [auth A],
N [auth A],
O [auth A],
PA [auth C],
QA [auth C],
RA [auth C],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth B],
YA [auth C],
ZA [auth D]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
FA [auth B]
GA [auth B]
HB [auth D]
IB [auth D]
P [auth A]
FA [auth B],
GA [auth B],
HB [auth D],
IB [auth D],
P [auth A],
Q [auth A],
SA [auth C],
TA [auth C]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CB [auth D]
DB [auth D]
K [auth A]
AA [auth B],
BA [auth B],
CB [auth D],
DB [auth D],
K [auth A],
L [auth A],
NA [auth C],
OA [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
R [auth A],
S [auth A],
T [auth A],
U [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth D],
J [auth A],
MA [auth C],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.57 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