+Open data
-Basic information
Entry | Database: PDB / ID: 5bkj | ||||||
---|---|---|---|---|---|---|---|
Title | TPeA-bound closed MthK channel in nanodisc | ||||||
Components | Calcium-gated potassium channel MthK | ||||||
Keywords | TRANSPORT PROTEIN / ion channel | ||||||
Function / homology | Function and homology information monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Fan, C. / Nimigean, C.M. | ||||||
Citation | Journal: Nat Chem Biol / Year: 2024 Title: Calcium-gated potassium channel blockade via membrane-facing fenestrations. Authors: Chen Fan / Emelie Flood / Nattakan Sukomon / Shubhangi Agarwal / Toby W Allen / Crina M Nimigean / 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 ...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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5bkj.cif.gz | 373.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5bkj.ent.gz | 307 KB | Display | PDB format |
PDBx/mmJSON format | 5bkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bkj_validation.pdf.gz | 1020 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5bkj_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5bkj_validation.xml.gz | 61.5 KB | Display | |
Data in CIF | 5bkj_validation.cif.gz | 84 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/5bkj ftp://data.pdbj.org/pub/pdb/validation_reports/bk/5bkj | HTTPS FTP |
-Related structure data
Related structure data | 9406MC 9405C 9407C 5bkiC 5bkkC 8djbC 8fz7C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 37356.160 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564 #2: Chemical | ChemComp-PGW / ( #3: Chemical | #4: Chemical | ChemComp-YQ1 / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: MthK / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Methanothermobacter thermautotrophicus (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 52.23 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement |
---|---|
CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C4 (4 fold cyclic) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80904 / Symmetry type: POINT |