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- EMDB-46421: Ca2+ bound open-inactivated hSlo1 + beta2N-beta4 channel in nanodisc. -

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Basic information

Entry
Database: EMDB / ID: EMD-46421
TitleCa2+ bound open-inactivated hSlo1 + beta2N-beta4 channel in nanodisc.
Map data
Sample
  • Complex: Ca2+ bound BK channel complex of hSlo1 + beta2N-beta4 subunit
    • Complex: Inactivating beta2N-beta4 subunit chimera
      • Protein or peptide: Isoform 5 of Calcium-activated potassium channel subunit alpha-1
    • Complex: hSlo1 channel
      • Protein or peptide: Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel subunit beta-4
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: POTASSIUM ION
KeywordsPotassium ion channel / calcium and voltage gated ion channel / big potassium channel / human BK / hSlo1 / open-inactivated hSlo1 / ball and chain inactivation / hSlo1 inactivating subunit complex / beta2 beta4 / nanodisc / membrane protein
Function / homology
Function and homology information


Acetylcholine inhibits contraction of outer hair cells / Ca2+ activated K+ channels / micturition / response to carbon monoxide / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / negative regulation of cell volume / regulation of neurotransmitter secretion / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / smooth muscle contraction involved in micturition ...Acetylcholine inhibits contraction of outer hair cells / Ca2+ activated K+ channels / micturition / response to carbon monoxide / large conductance calcium-activated potassium channel activity / calcium-activated potassium channel activity / negative regulation of cell volume / regulation of neurotransmitter secretion / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / 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 / action potential / voltage-gated potassium channel activity / detection of calcium ion / regulation of vasoconstriction / potassium channel regulator activity / neuronal action potential / voltage-gated potassium channel complex / potassium ion transmembrane transport / regulation of membrane potential / potassium ion transport / caveola / response to calcium ion / vasodilation / actin binding / monoatomic ion transmembrane transport / chemical synaptic transmission / postsynaptic membrane / response to hypoxia / apical plasma membrane / positive regulation of apoptotic process / synapse / metal ion binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
KCNMB2, ball/chain domain / KCNMB2, ball/chain domain superfamily / KCNMB2, ball and chain domain / Potassium channel, calcium-activated, BK, beta subunit / Calcium-activated potassium channel, beta subunit / : / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / Calcium-activated potassium channel BK, alpha subunit / : / : ...KCNMB2, ball/chain domain / KCNMB2, ball/chain domain superfamily / KCNMB2, ball and chain domain / Potassium channel, calcium-activated, BK, beta subunit / Calcium-activated potassium channel, beta subunit / : / Ca2+-activated K+ channel Slowpoke, TrkA_C like domain / Calcium-activated potassium channel BK, alpha subunit / : / : / Calcium-activated BK potassium channel alpha subunit / Calcium-activated potassium channel slowpoke-like RCK domain / RCK N-terminal domain profile. / Ion transport domain / Ion transport protein / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Large-conductance Ca2+-activated K+ channel beta2 subunit / Calcium-activated potassium channel subunit alpha-1 / Calcium-activated potassium channel subunit beta-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsAgarwal S / Nimigean C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: Nat Commun / Year: 2025
Title: Ball-and-chain inactivation of a human large conductance calcium-activated potassium channel.
Authors: Shubhangi Agarwal / Elizabeth D Kim / Sangyun Lee / Alexander Simon / Alessio Accardi / Crina M Nimigean /
Abstract: BK channels are large-conductance calcium (Ca)-activated potassium channels crucial for neuronal excitability, muscle contraction, and neurotransmitter release. The pore-forming (α) subunits co- ...BK channels are large-conductance calcium (Ca)-activated potassium channels crucial for neuronal excitability, muscle contraction, and neurotransmitter release. The pore-forming (α) subunits co-assemble with auxiliary (β and γ) subunits that modulate their function. Previous studies demonstrated that the N-termini of β2-subunits can inactivate BK channels, but with no structural correlate. Here, we investigate BK β2-subunit inactivation using cryo-electron microscopy, electrophysiology and molecular dynamics simulations. We find that the β2 N-terminus occludes the pore only in the Ca-bound open state, via a ball-and-chain mechanism. The first three hydrophobic residues of β2 are crucial for occlusion, while the remainder of the N-terminus remains flexible. Neither the closed channel conformation obtained in the absence of Ca nor an intermediate conformation found in the presence of Ca show density for the N-terminus of the β2 subunit in their pore, likely due to narrower side access portals preventing their entry into the channel pore.
History
DepositionAug 5, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46421.png

Downloads & links

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Map

FileDownload / File: emd_46421.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å		0.83 Å/pix.
x 300 pix.
= 247.5 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0126
Minimum - Maximum-0.018602015 - 0.060610037
Average (Standard dev.)0.00056972826 (±0.0032837684)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 247.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46421_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_46421_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_46421_half_map_2.map
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Sample components

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Entire : Ca2+ bound BK channel complex of hSlo1 + beta2N-beta4 subunit

EntireName: Ca2+ bound BK channel complex of hSlo1 + beta2N-beta4 subunit
Components
  • Complex: Ca2+ bound BK channel complex of hSlo1 + beta2N-beta4 subunit
    • Complex: Inactivating beta2N-beta4 subunit chimera
      • Protein or peptide: Isoform 5 of Calcium-activated potassium channel subunit alpha-1
    • Complex: hSlo1 channel
      • Protein or peptide: Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel subunit beta-4
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: MAGNESIUM ION
  • Ligand: CALCIUM ION
  • Ligand: CHOLESTEROL
  • Ligand: POTASSIUM ION

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Supramolecule #1: Ca2+ bound BK channel complex of hSlo1 + beta2N-beta4 subunit

SupramoleculeName: Ca2+ bound BK channel complex of hSlo1 + beta2N-beta4 subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Inactivating beta2N-beta4 subunit chimera

SupramoleculeName: Inactivating beta2N-beta4 subunit chimera / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: hSlo1 channel

SupramoleculeName: hSlo1 channel / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium...

MacromoleculeName: Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel subunit beta-4
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.431523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FIWTSGRTSS SYRHDEKRNI YQKIRDHDLL DKRKTVTALK AGEDKSIRLG LFLIISGVVS LFIFGFCWLS PALQDLQATE ANCTVLSVQ QIGEVFECTF TCGADCRGTS QYPCVQVYVN NSESNSRALL HSDEHQLLTN PKCSYIPPCK RENQKNLESV M NWQQYWKD ...String:
FIWTSGRTSS SYRHDEKRNI YQKIRDHDLL DKRKTVTALK AGEDKSIRLG LFLIISGVVS LFIFGFCWLS PALQDLQATE ANCTVLSVQ QIGEVFECTF TCGADCRGTS QYPCVQVYVN NSESNSRALL HSDEHQLLTN PKCSYIPPCK RENQKNLESV M NWQQYWKD EIGSQPFTCY FNQHQRPDDV LLHRTHDEIV LLHCFLWPLV TFVVGVLIVV LTICAKSLAV KAEAMKKRKF S

UniProtKB: Large-conductance Ca2+-activated K+ channel beta2 subunit, Calcium-activated potassium channel subunit beta-4

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Macromolecule #2: Isoform 5 of Calcium-activated potassium channel subunit alpha-1

MacromoleculeName: Isoform 5 of Calcium-activated potassium channel subunit alpha-1
type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.969945 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 RIKKCGCKRL EDEQPST LS PKKKQRNGGM RNSPNTSPKL MRHDPLLIPG NDQIDNMDSN VKKYDSTGMF HWCAPKEIEK VILTRSEAAM TVLSGHVV V CIFGDVSSAL IGLRNLVMPL RASNFHYHEL KHIVFVGSIE YLKREWETLH NFPKVSILPG TPLSRADLRA VNINLCDMC VILSANQNNI DDTSLQDKEC ILASLNIKSM QFDDSIGVLQ ANSQGFTPPG MDRSSPDNSP VHGMLRQPSI TTGVNIPIIT ELVNDTNVQ FLDQDDDDDP DTELYLTQPF ACGTAFAVSV LDSLMSATYF NDNILTLIRT LVTGGATPEL EALIAEENAL R GGYSTPQT LANRDRCRVA QLALLDGPFA DLGDGGCYGD LFCKALKTYN MLCFGIYRLR DAHLSTPSQC TKRYVITNPP YE FELVPTD LIFCLMQFD

UniProtKB: Calcium-activated potassium channel subunit alpha-1

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 32 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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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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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 8 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #7: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 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

Concentration9 mg/mL
BufferpH: 8
Details: 20 mM Tris-HCl pH 8.0, 450 mM KCl, 5 mM EDTA, 15 mM MgCl2, 0.02% GDN and 0.05 mg/ml POPE:POPC:POPA 5:5:1 (w:w:w).
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288.15 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) / Average electron dose: 48.45 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6v22

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 175971
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0.0)
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6v22


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9czm:
Ca2+ bound open-inactivated hSlo1 + beta2N-beta4 channel in nanodisc.

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