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- EMDB-39753: Activation mechanism and novel binding site of the BKCa channel a... -

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Basic information

Entry
Database: EMDB / ID: EMD-39753
TitleActivation mechanism and novel binding site of the BKCa channel activator CTIBD
Map data
Sample
  • Complex: Calcium-activated potassium channel subunit alpha-1 (Slo1)
    • Protein or peptide: Calcium-activated potassium channel subunit alpha-1
  • Ligand: 4-[4-(4-chlorophenyl)-3-(trifluoromethyl)-1,2-oxazol-5-yl]benzene-1,3-diol
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
KeywordsBKca channel / Slo1 / CTIBD / MEMBRANE PROTEIN
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / micturition / Ca2+ activated K+ channels / response to carbon monoxide / large conductance calcium-activated potassium channel activity / 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 / response to carbon monoxide / large conductance calcium-activated potassium channel activity / 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 / caveola / regulation of membrane potential / potassium ion transport / 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
: / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / : / Calcium-activated potassium channel BK, alpha subunit / Calcium-activated BK potassium channel alpha subunit / RCK N-terminal domain profile. / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Calcium-activated potassium channel subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsLee N / Kim S / Jo H / Lee NY / Jin MS / Park CS
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063908 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2022R1A2C1005532 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2021R1A6A3A01086747 Korea, Republic Of
CitationJournal: To Be Published
Title: Activation mechanism and novel binding site of the BKCa channel activator CTIBD
Authors: Lee N / Kim S / Jo H / Lee NY / Jeong P / Pagire HS / Pagire SH / Ahn JH / Jin MS / Park CS
History
DepositionApr 16, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39753.png

Downloads & links

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Map

FileDownload / File: emd_39753.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 200 pix.
= 282. Å		1.41 Å/pix.
x 200 pix.
= 282. Å		1.41 Å/pix.
x 200 pix.
= 282. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0829
Minimum - Maximum-0.75659114 - 0.89056385
Average (Standard dev.)-0.000000000000322 (±0.036177773)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 282.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_39753_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39753_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Calcium-activated potassium channel subunit alpha-1 (Slo1)

EntireName: Calcium-activated potassium channel subunit alpha-1 (Slo1)
Components
  • Complex: Calcium-activated potassium channel subunit alpha-1 (Slo1)
    • Protein or peptide: Calcium-activated potassium channel subunit alpha-1
  • Ligand: 4-[4-(4-chlorophenyl)-3-(trifluoromethyl)-1,2-oxazol-5-yl]benzene-1,3-diol
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Calcium-activated potassium channel subunit alpha-1 (Slo1)

SupramoleculeName: Calcium-activated potassium channel subunit alpha-1 (Slo1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: Calcium-activated potassium channel subunit alpha-1

MacromoleculeName: Calcium-activated potassium channel subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 125.541461 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDALIIPVTM EVPCDSRGQR MWWAFLASSM VTFFGGLFII LLWRTLKYLW TVCCHCGGKT KEAQKINNGS SQADGTLKPV DEKEEAVAA EVGWMTSVKD WAGVMISAQT LTGRVLVVLV FALSIGALVI YFIDSSNPIE SCQNFYKDFT LQIDMAFNVF F LLYFGLRF ...String:
MDALIIPVTM EVPCDSRGQR MWWAFLASSM VTFFGGLFII LLWRTLKYLW TVCCHCGGKT KEAQKINNGS SQADGTLKPV DEKEEAVAA EVGWMTSVKD WAGVMISAQT LTGRVLVVLV FALSIGALVI YFIDSSNPIE SCQNFYKDFT LQIDMAFNVF F LLYFGLRF IAANDKLWFW LEVNSVVDFF TVPPVFVSVY LNRSWLGLRF LRALRLIQFS EILQFLNILK TSNSIKLVNL LS IFISTWL TAAGFIHLVE NSGDPWENFQ NNQALTYWEC VYLLMVTMST VGYGDVYAKT TLGRLFMVFF ILGGLAMFAS YVP EIIELI GNRKKYGGSY SAVSGRKHIV VCGHITLESV SNFLKDFLHK DRDDVNVEIV FLHNISPNLE LEALFKRHFT QVEF YQGSV LNPHDLARVK IESADACLIL ANKYCADPDA EDASNIMRVI SIKNYHPKIR IITQMLQYHN KAHLLNIPSW NWKEG DDAI CLAELKLGFI AQSCLAQGLS TMLANLFSMR SFIKIEEDTW QKYYLEGVSN EMYTEYLSSA FVGLSFPTVC ELCFVK LKL LMIAIEYKSA NRESRILINP GNHLKIQEGT LGFFIASDAK EVKRAFFYCK ACHDDITDPK RIKKCGCKRP KMSIYKR MR RACCFDCGRS ERDCSCMSGR VRGNVDTLER AFPLSSVSVN DCSTSFRAFE DEQPSTLSPK KKQRNGGMRN SPNTSPKL M RHDPLLIPGN DQIDNMDSNV KKYDSTGMFH WCAPKEIEKV ILTRSEAAMT VLSGHVVVCI FGDVSSALIG LRNLVMPLR ASNFHYHELK HIVFVGSIEY LKREWETLHN FPKVSILPGT PLSRADLRAV NINLCDMCVI LSANQNNIDD TSLQDKECIL ASLNIKSMQ FDDSIGVLQA NSQGFTPPGM DRSSPDNSPV HGMLRQPSIT TGVNIPIITE LVNDTNVQFL DQDDDDDPDT E LYLTQPFA CGTAFAVSVL DSLMSATYFN DNILTLIRTL VTGGATPELE ALIAEENALR GGYSTPQTLA NRDRCRVAQL AL LDGPFAD LGDGGCYGDL FCKALKTYNM LCFGIYRLRD AHLSTPSQCT KRYVITNPPY EFELVPTDLI FCLMQFD

UniProtKB: Calcium-activated potassium channel subunit alpha-1

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Macromolecule #2: 4-[4-(4-chlorophenyl)-3-(trifluoromethyl)-1,2-oxazol-5-yl]benzene...

MacromoleculeName: 4-[4-(4-chlorophenyl)-3-(trifluoromethyl)-1,2-oxazol-5-yl]benzene-1,3-diol
type: ligand / ID: 2 / Number of copies: 8 / Formula: A1L04
Molecular weightTheoretical: 355.696 Da

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris hydrochloride
450.0 mMKClPotassium chloride
10.0 mMCaCl2Calcium chloride
0.01 %GDNGlyco-diosgenin
0.045 mg/mlPOPC1-palmitoyl-2-oleoyl-glycero-3-phosphocholine
0.045 mg/mlPOPE1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine
0.01 mg/mlPOPA1-palmitoyl-2-oleoyl-sn-glycero-3-phosphate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4806 / Average exposure time: 13.67 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 73000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 700885
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Non-uniform Refinement / Number images used: 288878
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.3.2) / Software - details: Heterogeneous Refinement

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Atomic model buiding 1

Initial modelPDB ID:

6v38


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8z3s:
Activation mechanism and novel binding site of the BKCa channel activator CTIBD

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