5BKI

Blocker-free closed MthK channel in nanodisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Calcium-gated potassium channel blockade via membrane-facing fenestrations.

Fan, C.Flood, E.Sukomon, N.Agarwal, S.Allen, T.W.Nimigean, C.M.

(2023) Nat Chem Biol 

  • DOI: https://doi.org/10.1038/s41589-023-01406-2
  • Primary Citation of Related Structures:  
    5BKI, 5BKJ, 5BKK, 8DJB, 8FZ7

  • PubMed Abstract: 

    Quaternary ammonium blockers were previously shown to bind in the pore to block both open and closed conformations of large-conductance calcium-activated potassium (BK and MthK) channels. Because blocker entry was assumed through the intracellular entryway (bundle crossing), closed-pore access suggested that the gate was not at the bundle crossing. Structures of closed MthK, a Methanobacterium thermoautotrophicum homolog of BK channels, revealed a tightly constricted intracellular gate, leading us to investigate the membrane-facing fenestrations as alternative pathways for blocker access directly from the membrane. Atomistic free energy simulations showed that intracellular blockers indeed access the pore through the fenestrations, and a mutant channel with narrower fenestrations displayed no closed-state TPeA block at concentrations that blocked the wild-type channel. Apo BK channels display similar fenestrations, suggesting that blockers may use them as access paths into closed channels. Thus, membrane fenestrations represent a non-canonical pathway for selective targeting of specific channel conformations, opening novel ways to selectively drug BK channels.


  • Organizational Affiliation

    Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calcium-gated potassium channel MthK336Methanothermobacter thermautotrophicusMutation(s): 0 
Gene Names: mthKMTH_1520
Membrane Entity: Yes 
UniProt
Find proteins for O27564 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O27564 
Go to UniProtKB:  O27564
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO27564
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGW (Subject of Investigation/LOI)
Query on PGW

Download Ideal Coordinates CCD File 
J [auth A],
Q [auth C],
S [auth E],
U [auth G]
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
PAZGBAOHGQRCBP-HGWHEPCSSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth H]
CA [auth H]
I [auth A]
P [auth C]
AA [auth F],
BA [auth H],
CA [auth H],
I [auth A],
P [auth C],
R [auth E],
T [auth G],
V [auth B],
W [auth B],
X [auth D],
Y [auth D],
Z [auth F]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Structure summary