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Yorodumi- PDB-8z3s: Activation mechanism and novel binding site of the BKCa channel a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8z3s | ||||||||||||
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Title | Activation mechanism and novel binding site of the BKCa channel activator CTIBD | ||||||||||||
Components | Calcium-activated potassium channel subunit alpha-1 | ||||||||||||
Keywords | MEMBRANE PROTEIN / BKca channel / Slo1 / CTIBD | ||||||||||||
Function / homology | Function and homology information Acetylcholine inhibits contraction of outer hair cells / micturition / Ca2+ activated K+ channels / large conductance calcium-activated potassium channel activity / response to carbon monoxide / calcium-activated potassium channel activity / negative regulation of cell volume / smooth muscle contraction involved in micturition / intracellular potassium ion homeostasis / Sensory processing of sound by inner hair cells of the cochlea ...Acetylcholine inhibits contraction of outer hair cells / micturition / Ca2+ activated K+ channels / large conductance calcium-activated potassium channel activity / response to carbon monoxide / calcium-activated potassium channel activity / negative regulation of cell volume / smooth muscle contraction involved in micturition / intracellular potassium ion homeostasis / Sensory processing of sound by inner hair cells of the cochlea / response to osmotic stress / cGMP effects / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / caveola / response to calcium ion / vasodilation / actin binding / postsynaptic membrane / response to hypoxia / positive regulation of apoptotic process / apical plasma membrane / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Lee, N. / Kim, S. / Jo, H. / Lee, N.Y. / Jin, M.S. / Park, C.S. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Life Sci Alliance / Year: 2024 Title: Activation mechanism and novel binding sites of the BK channel activator CTIBD. Authors: Narasaem Lee / Subin Kim / Na Young Lee / Heeji Jo / Pyeonghwa Jeong / Haushabhau S Pagire / Suvarna H Pagire / Jin Hee Ahn / Mi Sun Jin / Chul-Seung Park / Abstract: The large-conductance calcium-activated potassium (BK) channel, which is crucial for urinary bladder smooth muscle relaxation, is a potential target for overactive bladder treatment. Our prior work ...The large-conductance calcium-activated potassium (BK) channel, which is crucial for urinary bladder smooth muscle relaxation, is a potential target for overactive bladder treatment. Our prior work unveiled CTIBD as a promising BK channel activator, altering and This study investigates CTIBD's activation mechanism, revealing its independence from the Ca and membrane voltage sensing of the BK channel. Cryo-electron microscopy disclosed that two CTIBD molecules bind to hydrophobic regions on the extracellular side of the lipid bilayer. Key residues (W22, W203, and F266) are important for CTIBD binding, and their replacement with alanine reduces CTIBD-mediated channel activation. The triple-mutant (W22A/W203A/F266A) channel showed the smallest shift with a minimal impact on activation and deactivation kinetics by CTIBD. At the single-channel level, CTIBD treatment was much less effective at increasing in the triple mutant, mainly because of a drastically increased dissociation rate compared with the WT. These findings highlight CTIBD's mechanism, offering crucial insights for developing small-molecule treatments for BK-related pathophysiological conditions. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8z3s.cif.gz | 652.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8z3s.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8z3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8z3s_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8z3s_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8z3s_validation.xml.gz | 100.9 KB | Display | |
Data in CIF | 8z3s_validation.cif.gz | 149.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/8z3s ftp://data.pdbj.org/pub/pdb/validation_reports/z3/8z3s | HTTPS FTP |
-Related structure data
Related structure data | 39753MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 125541.461 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KCNMA1, KCNMA, SLO / Cell line (production host): HEK293S GnTi / Production host: Homo sapiens (human) / References: UniProt: Q12791 #2: Chemical | ChemComp-A1L04 / Mass: 355.696 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H9ClF3NO3 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-Y01 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CA / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Calcium-activated potassium channel subunit alpha-1 (Slo1) Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.5 MDa / Experimental value: YES | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293S GnTi / Plasmid: pEG Bacman | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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 / Nominal magnification: 73000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 13.67 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 4806 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 700885 | |||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C4 (4 fold cyclic) | |||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288878 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6V38 Accession code: 6V38 / Source name: PDB / Type: experimental model | |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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