8Z3S

Activation mechanism and novel binding site of the BKCa channel activator CTIBD

PDB DOI: https://doi.org/10.2210/pdb8Z3S/pdb
EM Map EMD-39753: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-04-16 Released: 2024-07-31
Deposition Author(s): Lee, N., Kim, S., Jo, H., Lee, N.Y., Jin, M.S., Park, C.S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 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

Activation mechanism and novel binding site of the BKCa channel activator CTIBD

Lee, N., Kim, S., Jo, H., Lee, N.Y., Jeong, P., Pagire, H.S., Pagire, S.H., Ahn, J.H., Jin, M.S., Park, C.S.

To be published.

Macromolecule Content

Total Structure Weight: 507.38 kDa
Atom Count: 29,005
Modelled Residue Count: 3,600
Deposited Residue Count: 4,456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcium-activated potassium channel subunit alpha-1	A, B, C, D	1,114	Homo sapiens	Mutation(s): 0 Gene Names: KCNMA1, KCNMA, SLO
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12791
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain S [auth C] SDF format, chain Y [auth D] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D]	G [auth A], M [auth B], S [auth C], Y [auth D]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain S [auth C] Focus chain Y [auth D]
A1L04 (Subject of Investigation/LOI) Query on A1L04 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D]	E [auth A] F [auth A] K [auth B] L [auth B] Q [auth C] E [auth A], F [auth A], K [auth B], L [auth B], Q [auth C], R [auth C], W [auth D], X [auth D]	4-[4-(4-chlorophenyl)-3-(trifluoromethyl)-1,2-oxazol-5-yl]benzene-1,3-diol C₁₆ H₉ Cl F₃ N O₃ BYNUBBWBGHJHNP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain W [auth D] Focus chain X [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C]	AA [auth D] BA [auth D] I [auth A] J [auth A] O [auth B] AA [auth D], BA [auth D], I [auth A], J [auth A], O [auth B], P [auth B], U [auth C], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D]	H [auth A], N [auth B], T [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	3.3.2
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2019M3E5D6063908
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2022R1A2C1005532
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A6A3A01086747