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- EMDB-48725: Structure of Xenopus KCNQ1-CaM in GDN -

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Basic information

Entry
Database: EMDB / ID: EMD-48725
TitleStructure of Xenopus KCNQ1-CaM in GDN
Map data
Sample
  • Complex: Potassium voltage-gated channel subfamily KQT member 1 in complex with calmodulin
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 1
    • Protein or peptide: Calmodulin-1
KeywordsPotassium Ion Channel Protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


regulation of gastric acid secretion / membrane repolarization / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / intestinal absorption / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels ...regulation of gastric acid secretion / membrane repolarization / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / intestinal absorption / 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 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / monoatomic ion channel complex / renal absorption / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / autophagosome membrane docking / inner ear development / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / regulation of cell communication by electrical coupling involved in cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / voltage-gated potassium channel activity / detection of calcium ion / catalytic complex / regulation of cardiac muscle contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / presynaptic cytosol / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / Protein methylation / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol-4,5-bisphosphate binding / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / potassium ion transmembrane transport / regulation of heart rate / FCGR3A-mediated IL10 synthesis / cytoplasmic vesicle membrane / calyx of Held / Ras activation upon Ca2+ influx through NMDA receptor / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / adenylate cyclase activator activity / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / Transcriptional activation of mitochondrial biogenesis / RAF activation / response to calcium ion / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Stimuli-sensing channels / long-term synaptic potentiation / spindle pole / calcium-dependent protein binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / RAS processing / Signaling by BRAF and RAF1 fusions
Similarity search - Function
Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...Potassium channel, voltage dependent, KCNQ1 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Voltage-dependent channel domain superfamily / : / 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 / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsKyriakis E / Russo S / Molinarolo S / Eldstrom J / Van Petegem F / Fedida D
Funding support Canada, 6 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-156181 Canada
Canadian Institutes of Health Research (CIHR)PJT-518041 Canada
Other governmentG-21-0031566
Other governmentG-24-0036478
Canadian Institutes of Health Research (CIHR)PJT-153305 Canada
Other governmentRT-2022-2735
CitationJournal: Nat Commun / Year: 2025
Title: A physiologically-relevant intermediate state structure of a voltage-gated potassium channel.
Authors: Efthimios Kyriakis / Daniel Sastre / Jodene Eldstrom / Agnese Roscioni / Sophia Russo / Fariba Ataei / Ying Dou / Magnus Chan / Steven Molinarolo / Luca Maragliano / Filip Van Petegem / David Fedida /
Abstract: Voltage-gated potassium ion (K) channels perform critical roles in many physiological processes, while gain- or loss-of-function mutations lead to life-threatening pathologies. Here, we establish the ...Voltage-gated potassium ion (K) channels perform critical roles in many physiological processes, while gain- or loss-of-function mutations lead to life-threatening pathologies. Here, we establish the high-resolution structure of a pivotal intermediate state of the Kv7.1 (KCNQ1) channel using cryogenic electron microscopy. The 3.53 Å resolution structure reveals straightened upper S1 and S2 voltage sensor helices, distancing them from the pore filter helix compared to fully activated channels. The outward translation of the S4 voltage sensor is essentially complete in this intermediate state, and the S4-S6 helices and the S4-S5 linker do not change position significantly between intermediate and activated states. The PIP2 ligand can bind in both states. Movement of S1 and S2 helices towards the filter helix from intermediate to activated states may explain smaller components of KCNQ1 voltage sensor fluorescence, differential Rb/K selectivity, and pharmacological responses to activators and inhibitors. Single channel recordings and the location of long QT mutations suggest the potential physiological and disease importance of the intermediate state.
History
DepositionJan 21, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48725.png

Downloads & links

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Map

FileDownload / File: emd_48725.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 336 pix.
= 322.56 Å		0.96 Å/pix.
x 336 pix.
= 322.56 Å		0.96 Å/pix.
x 336 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.093
Minimum - Maximum-0.24885735 - 0.5297463
Average (Standard dev.)0.00070042734 (±0.014681865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_48725_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_48725_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Potassium voltage-gated channel subfamily KQT member 1 in complex...

EntireName: Potassium voltage-gated channel subfamily KQT member 1 in complex with calmodulin
Components
  • Complex: Potassium voltage-gated channel subfamily KQT member 1 in complex with calmodulin
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 1
    • Protein or peptide: Calmodulin-1

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Supramolecule #1: Potassium voltage-gated channel subfamily KQT member 1 in complex...

SupramoleculeName: Potassium voltage-gated channel subfamily KQT member 1 in complex with calmodulin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 317.56 KDa

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Macromolecule #1: Potassium voltage-gated channel subfamily KQT member 1

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 1
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 62.375137 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATDPPRPTI NLDPRVSIYS GRRPLLSRTN IQGRVYNFLE RPTGWKCFVY HFTVFLIVLI CLIFSVLSTI QQYNNLATET LFWMEIVLV VFFGAEYVVR LWSAGCRSKY VGVWGRLRFA RKPISVIDLI VVVASVIVLC VGSNGQVFAT SAIRGIRFLQ I LRMLHVDR ...String:
MATDPPRPTI NLDPRVSIYS GRRPLLSRTN IQGRVYNFLE RPTGWKCFVY HFTVFLIVLI CLIFSVLSTI QQYNNLATET LFWMEIVLV VFFGAEYVVR LWSAGCRSKY VGVWGRLRFA RKPISVIDLI VVVASVIVLC VGSNGQVFAT SAIRGIRFLQ I LRMLHVDR QGGTWRLLGS VVFIHRQELI TTLYIGFLGL IFSSYFVYLA EKDAIDSSGE YQFGSYADAL WWGVVTVTTI GY GDKVPQT WIGKTIASCF SVFAISFFAL PAGILGSGFA LKVQQKQRQK HFNRQIPAAA SLIQTAWRCY AAENPDSATW KIY IRKQSR NHHLMSPSPK PKKSAMVKKK KIRTERDEGS TDKMLNIPHI TYDHVADDRK NDGYSVESYE NTVRKPFGFL DPST GPFIR TSSFTDDLDM EGDTLLTPIT HISELKEHHR AAIKVIRRMQ YFVAKKKFQQ ARKPYDVRDV IEQYSQGHLN LMVRI KELQ RRLDQSLGKP SLFLSVSDKV KDKGINTIGS RLNRVEDKVT QMDHKLNLIT DMLHHLLTNQ Q

UniProtKB: Potassium voltage-gated channel subfamily KQT member 1

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
150.0 mMKClpotassium chloride
20.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
2.0 mMDithiothreitol
4.0 mMEGTA
0.03 %glyco-diosgenin
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5500 / 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
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: 1348161
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 47918
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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