[English] 日本語
Yorodumi
- EMDB-46423: Ca2+ bound intermediate state of hSlo1 + beta2N-beta4 channel in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46423
TitleCa2+ bound intermediate state of 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: Large-conductance Ca2+-activated K+ channel beta2 subunit,Calcium-activated potassium channel subunit beta-4
    • Complex: hSlo1 channel
      • Protein or peptide: Isoform 5 of Calcium-activated potassium channel subunit alpha-1
  • Ligand: CALCIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsPotassium ion channel / calcium and voltage gated ion channel / big potassium channel / human BK / hSlo1 / intermediate hSlo1 / ball and chain inactivation / hSlo1 inactivating subunit complex / nanodisc / membrane protein / beta2 / beta4
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: 2.87 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

-
Structure visualization

Supplemental images

emd_46423.png

Downloads & links

-
Map

FileDownload / File: emd_46423.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0102
Minimum - Maximum-0.010355023 - 0.042495027
Average (Standard dev.)0.00046953798 (±0.0025610942)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_46423_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_46423_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_46423_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

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

-
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)

-
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)

-
Supramolecule #3: hSlo1 channel

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

-
Macromolecule #1: 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: 1 / 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

-
Macromolecule #2: 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: 2 / 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

-
Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: CA
Molecular weightTheoretical: 40.078 Da

-
Macromolecule #4: POTASSIUM ION

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

-
Macromolecule #5: (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: 5 / Number of copies: 11 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

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

6v35

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 154169
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)

-
Atomic model buiding 1

Initial modelPDB ID:

6v35


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

PDB-9czo:
Ca2+ bound intermediate state of hSlo1 + beta2N-beta4 channel in nanodisc.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more