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- EMDB-70121: Cryo-EM structure of the human SK2-4 chimera/calmodulin channel c... -

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Basic information

Entry
Database: EMDB / ID: EMD-70121
TitleCryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to the bee toxin apamin
Map dataUnsharpened map
Sample
  • Complex: Ternary complex of human SK2-4 chimera/calmodulin channel complex bound to the bee toxin apamin
    • Complex: Human SK2-4 chimeric channel
      • Protein or peptide: Intermediate conductance calcium-activated potassium channel protein 4,Small conductance calcium-activated potassium channel protein 2 chimera
    • Complex: Human calmodulin
      • Protein or peptide: Calmodulin-1
    • Complex: Apamin
      • Protein or peptide: Apamin
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
KeywordsIon channel / Toxin / Apamin / Potassium / TRANSPORT PROTEIN-TOXIN complex
Function / homology
Function and homology information


venom-mediated perturbation of biological process / negative regulation of inward rectifier potassium channel activity / inward rectifier potassium channel inhibitor activity / intermediate conductance calcium-activated potassium channel activity / saliva secretion / small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / membrane repolarization during atrial cardiac muscle cell action potential / stabilization of membrane potential / Ca2+ activated K+ channels ...venom-mediated perturbation of biological process / negative regulation of inward rectifier potassium channel activity / inward rectifier potassium channel inhibitor activity / intermediate conductance calcium-activated potassium channel activity / saliva secretion / small conductance calcium-activated potassium channel activity / Acetylcholine inhibits contraction of outer hair cells / membrane repolarization during atrial cardiac muscle cell action potential / stabilization of membrane potential / Ca2+ activated K+ channels / macropinocytosis / negative regulation of potassium ion transmembrane transport / calcium-activated potassium channel activity / negative regulation of potassium ion transmembrane transporter activity / potassium channel inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of potassium ion transmembrane transport / inward rectifier potassium channel activity / cell volume homeostasis / regulation of potassium ion transmembrane transport / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / phospholipid translocation / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / positive regulation of ryanodine-sensitive calcium-release channel activity / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / negative regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / positive regulation of T cell receptor signaling pathway / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / alpha-actinin binding / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / protein phosphatase activator activity / DARPP-32 events / Smooth Muscle Contraction / immune system process / catalytic complex / potassium channel activity / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / potassium ion transmembrane transport / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / positive regulation of protein secretion / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT
Similarity search - Function
Honey bee toxin / Honey bee toxin / Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Potassium channel domain / Ion channel ...Honey bee toxin / Honey bee toxin / Calmodulin-binding domain / Potassium channel, calcium-activated, SK / SK, calmodulin-binding domain superfamily / Calmodulin binding domain / Calcium-activated SK potassium channel / Calmodulin binding domain / Potassium channel domain / Ion channel / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Intermediate conductance calcium-activated potassium channel protein 4 / Apamin / Calmodulin-1 / Small conductance calcium-activated potassium channel protein 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Apis mellifera (honey bee)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsCassell SJ / Khoshouei M / Wilhelm WA / Whicher JR
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mechanism of SK2 channel gating and its modulation by the bee toxin apamin and small molecules
Authors: Cassell SJ / Li W / Krautwald S / Khoshouei M / Lee YT / Hou J / Guan W / Peukert S / Wilhelm WA / Whicher JR
History
DepositionApr 9, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70121.png

Downloads & links

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Map

FileDownload / File: emd_70121.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 304.2 Å		0.85 Å/pix.
x 360 pix.
= 304.2 Å		0.85 Å/pix.
x 360 pix.
= 304.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.845 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.1558833 - 3.4750078
Average (Standard dev.)-0.0002615511 (±0.0707322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_70121_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_70121_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70121_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of human SK2-4 chimera/calmodulin channel complex...

EntireName: Ternary complex of human SK2-4 chimera/calmodulin channel complex bound to the bee toxin apamin
Components
  • Complex: Ternary complex of human SK2-4 chimera/calmodulin channel complex bound to the bee toxin apamin
    • Complex: Human SK2-4 chimeric channel
      • Protein or peptide: Intermediate conductance calcium-activated potassium channel protein 4,Small conductance calcium-activated potassium channel protein 2 chimera
    • Complex: Human calmodulin
      • Protein or peptide: Calmodulin-1
    • Complex: Apamin
      • Protein or peptide: Apamin
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION

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Supramolecule #1: Ternary complex of human SK2-4 chimera/calmodulin channel complex...

SupramoleculeName: Ternary complex of human SK2-4 chimera/calmodulin channel complex bound to the bee toxin apamin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Human SK2-4 chimeric channel

SupramoleculeName: Human SK2-4 chimeric channel / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Human calmodulin

SupramoleculeName: Human calmodulin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: Apamin

SupramoleculeName: Apamin / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: Purchased from Millipore Sigma #178270
Source (natural)Organism: Apis mellifera (honey bee)

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Macromolecule #1: Intermediate conductance calcium-activated potassium channel prot...

MacromoleculeName: Intermediate conductance calcium-activated potassium channel protein 4,Small conductance calcium-activated potassium channel protein 2 chimera
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.382164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGGDLVLGLG ALRRRRALFE KRKRLSDYAL IFGMFGIVVM VIETELSWGA YDKASLYSLA LKCLISLSTI ILLGLIIVYH AREIQLFMV DNGADDWRIA MTYERIFFIC LEILVCAIHP IPGNYTFTWT ARLAFSYAPS TTTADVDIIL SIPMFLRLYL I ARVMLLHS ...String:
MGGDLVLGLG ALRRRRALFE KRKRLSDYAL IFGMFGIVVM VIETELSWGA YDKASLYSLA LKCLISLSTI ILLGLIIVYH AREIQLFMV DNGADDWRIA MTYERIFFIC LEILVCAIHP IPGNYTFTWT ARLAFSYAPS TTTADVDIIL SIPMFLRLYL I ARVMLLHS KLFTDASSRS IGALNKINFN TRFVMKTLMT ICPGTVLLVF SISLWIIAAW TVRACERYHD QQDVTSNFLG AM WLISITF LSIGYGDMVP NTYCGKGVCL LTGIMGAGCT ALVVAVVARK LELTKAEKHV HNFMMDIQYT KEMKESAARV LQE AWMFYK HTRRKESHAA RRHQRKLLAA INAFRQVRLK HRKLREQVNS MVDISKMHMI LYDLQQNLSS SHRALEKQID TLAG KLDAL TELLSTALGP RQLPEPSQQS KSSSLEVLFQ

UniProtKB: Intermediate conductance calcium-activated potassium channel protein 4, Small conductance calcium-activated potassium channel protein 2, Intermediate conductance calcium-activated potassium channel protein 4

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #3: Apamin

MacromoleculeName: Apamin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Apis mellifera (honey bee)
Molecular weightTheoretical: 2.036385 KDa
SequenceString:
CNCKAPETAL CARRCQQH

UniProtKB: Apamin

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Macromolecule #4: POTASSIUM ION

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

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 16 / 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

Concentration7.5 mg/mL
BufferpH: 8
Details: 20 mM Tris pH 8, 150 mM KCl, 2 mM CaCl2, 0.005% GDN, 0.0005% CHS
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.05 kPa
Details: UltrAuFoil R 1.2/1.3 300 mesh grids were glow-discharged for 30 seconds at 0.5 mBar with 15 mA using easiGlow system
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: 5 uL of sample was applied to grids at 4 degree temperature with 100% humidity. After 30 seconds, grids were blotted for 5 seconds with blot force 25 and plunged into liquid ethane..

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope has a Cs corrector
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 15779 / Average exposure time: 3.25 sec. / Average electron dose: 50.0 e/Å2
Details: Images were collected in EER format with 50 fractions
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7500000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab initio model generated during processing
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 734192
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

9o48

source_name: PDB, initial_model_type: experimental model

7oxf

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL
Output model

PDB-9o52:
Cryo-EM structure of the human SK2-4 chimera/calmodulin channel complex bound to the bee toxin apamin

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