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- PDB-10nk: Xenopus KCNQ1 Intermediate State (E1R/R2E) in complex with UCL2077 -

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Basic information

Entry
Database: PDB / ID: 10nk
TitleXenopus KCNQ1 Intermediate State (E1R/R2E) in complex with UCL2077
Components
  • Calmodulin-1
  • Potassium voltage-gated channel subfamily KQT member 1
KeywordsTRANSPORT PROTEIN / Potassium Ion Channel Protein
Function / homology
Function and homology information


regulation of gastric acid secretion / membrane repolarization / intestinal absorption / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels ...regulation of gastric acid secretion / membrane repolarization / intestinal absorption / delayed rectifier potassium channel activity / outward rectifier potassium channel activity / 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 / PKA activation / CaMK IV-mediated phosphorylation of CREB / inner ear development / CASP4 inflammasome assembly / 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 / : / negative regulation of high voltage-gated calcium channel activity / autophagosome membrane docking / 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 / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / catalytic complex / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / voltage-gated potassium channel activity / regulation of cardiac muscle contraction / cellular response to interferon-beta / RHO GTPases activate IQGAPs / calcium channel inhibitor activity / presynaptic cytosol / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of heart rate / 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 / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / FCGR3A-mediated IL10 synthesis / potassium ion transmembrane transport / protein serine/threonine kinase activator activity / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / cytoplasmic vesicle membrane / calyx of Held / positive regulation of receptor signaling pathway via JAK-STAT / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / regulation of cytokinesis / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / spindle microtubule / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / myelin sheath / cellular response to type II interferon / Transcriptional activation of mitochondrial biogenesis / long-term synaptic potentiation / Enterobacterial factors antagonize host defense / response to calcium ion / RAF activation / Stimuli-sensing channels / 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
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 / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
: / Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsKyriakis, E. / Eldstrom, J. / Van Petegem, F. / Fedida, D.
Funding support Canada, 7items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-174999 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-03021 Canada
Canadian Institutes of Health Research (CIHR)PJT-156181 Canada
Canadian Institutes of Health Research (CIHR)PJT-518041 Canada
Other privateG-21-0031566
Other privateG-24-0036478
Other governmentRT-2022-2735
CitationJournal: Sci Adv / Year: 2026
Title: Structural and kinetic mechanisms of state-dependent potassium channel inhibition
Authors: Kyriakis, E. / Roscioni, A. / Eldstrom, J. / Sastre, D. / Dou, Y. / Taddei, A. / Molinarolo, S. / Tian, M. / Maragliano, L. / Van Petegem, F. / Fedida, D.
History
DepositionJan 28, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Calmodulin-1
D: Calmodulin-1
A: Potassium voltage-gated channel subfamily KQT member 1
G: Potassium voltage-gated channel subfamily KQT member 1
C: Calmodulin-1
E: Calmodulin-1
F: Potassium voltage-gated channel subfamily KQT member 1
H: Potassium voltage-gated channel subfamily KQT member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,61210
Polymers316,9118
Non-polymers7012
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "C" or chain "E" or chain "F" or chain "H" or chain "J"
d_2ens_1chain "A" or chain "B" or chain "D" or chain "G" or chain "I"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILEMETMETCE10 - 14610 - 146
d_12ILEILEMETMETEF10 - 14610 - 146
d_13ASNASNGLNGLNFG95 - 54930 - 484
d_14ASNASNGLNGLNHH95 - 54930 - 484
d_15A1C6WA1C6WA1C6WA1C6WFJ701
d_21ILEILEMETMETBA10 - 14610 - 146
d_22ILEILEMETMETDB10 - 14610 - 146
d_23ASNASNGLNGLNAC95 - 54930 - 484
d_24ASNASNGLNGLNGD95 - 54930 - 484
d_25A1C6WA1C6WA1C6WA1C6WAI701

NCS oper: (Code: given
Matrix: (-1, -1.31682696127E-7, -1.22288623792E-8), (1.31682696198E-7, -1, -5.84122550976E-9), (-1.222886161E-8, -5.84122712009E-9, 1)
Vector: 345.599025955, 345.600860053, 3.34871228347E-6)

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Components

#1: Protein
Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Cell line (production host): tsA201 / Production host: Homo sapiens (human) / References: UniProt: P0DP23
#2: Protein
Potassium voltage-gated channel subfamily KQT member 1 / IKs producing slow voltage-gated potassium channel subunit alpha xKvLQT1 / KQT-like 1 / Voltage- ...IKs producing slow voltage-gated potassium channel subunit alpha xKvLQT1 / KQT-like 1 / Voltage-gated potassium channel subunit Kv7.1


Mass: 62375.137 Da / Num. of mol.: 4 / Mutation: E150R, R221E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: kcnq1, kvlqt1 / Cell line (production host): tsA201 / Production host: Homo sapiens (human) / References: UniProt: P70057
#3: Chemical ChemComp-A1C6W / 1,1,1-triphenyl-N-[(pyridin-3-yl)methyl]methanamine


Mass: 350.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H22N2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Potassium voltage-gated channel subfamily KQT member 1 (E150R/R221E) in complex with calmodulin and UCL2077
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.31756 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMpotassium chlorideKCl1
220 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
32 mMDithiothreitol1
44 mMEGTA1
50.03 %glyco-diosgenin1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 14687
EM imaging opticsEnergyfilter name: TFS Selectris

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPUimage acquisition
4cryoSPARC4.6.0CTF correction
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3155378
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57405 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 178.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003314830
ELECTRON MICROSCOPYf_angle_d0.829820126
ELECTRON MICROSCOPYf_chiral_restr0.04272284
ELECTRON MICROSCOPYf_plane_restr0.00392556
ELECTRON MICROSCOPYf_dihedral_angle_d5.44452044
Refine LS restraints NCSType: NCS constraints / Rms dev position: 1.10808634506E-12 Å

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