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- PDB-22bf: XEN1101 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 2 -

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Basic information

Entry
Database: PDB / ID: 22bf
TitleXEN1101 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 2
Components
  • Potassium voltage-gated channel subfamily KQT member 2
  • Potassium voltage-gated channel subfamily KQT member 3
KeywordsMEMBRANE PROTEIN / M-channel / KCNQ2/3 / heteromeric channel / cryoEM / XEN1101
Function / homology
Function and homology information


apoptosome assembly / regulation of action potential firing threshold / inhibitory chemical synaptic transmission / substantia propria of cornea development / action potential initiation / excitatory chemical synaptic transmission / nerve development / mitochondrial depolarization / response to auditory stimulus / psychomotor behavior ...apoptosome assembly / regulation of action potential firing threshold / inhibitory chemical synaptic transmission / substantia propria of cornea development / action potential initiation / excitatory chemical synaptic transmission / nerve development / mitochondrial depolarization / response to auditory stimulus / psychomotor behavior / axon initial segment / Voltage gated Potassium channels / node of Ranvier / membrane hyperpolarization / Interaction between L1 and Ankyrins / ankyrin binding / voltage-gated monoatomic cation channel activity / neuron remodeling / exocytosis / action potential / voltage-gated potassium channel activity / protein targeting / neuronal action potential / voltage-gated potassium channel complex / potassium ion transmembrane transport / cellular response to calcium ion / sensory perception of sound / regulation of synaptic plasticity / cellular response to xenobiotic stimulus / endocytosis / protein import into nucleus / nervous system development / neuron apoptotic process / gene expression / chemical synaptic transmission / calmodulin binding / synapse / cell surface / mitochondrion / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, KCNQ3 / Potassium channel, voltage dependent, KCNQ2 / Unstructured region on Potassium channel subunit alpha KvLQT2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Potassium channel, voltage dependent, KCNQ / Potassium channel, voltage dependent, KCNQ, C-terminal / KCNQ voltage-gated potassium channel / Ion transport domain / Ion transport protein
Similarity search - Domain/homology
: / : / Potassium voltage-gated channel subfamily KQT member 3 / Potassium voltage-gated channel subfamily KQT member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLu, F. / Fan, X. / Huang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32501082 China
CitationJournal: To Be Published
Title: Structural basis for the assembly and modulation of human M-channels
Authors: Lu, F. / Huang, X. / Cai, G. / Xie, Y. / Fan, X. / Huang, J.
History
DepositionJan 5, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 3, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily KQT member 3
B: Potassium voltage-gated channel subfamily KQT member 2
C: Potassium voltage-gated channel subfamily KQT member 2
D: Potassium voltage-gated channel subfamily KQT member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,38811
Polymers384,7974
Non-polymers1,5917
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Potassium voltage-gated channel subfamily KQT member 3 / KQT-like 3 / Potassium channel subunit alpha KvLQT3 / Voltage-gated potassium channel subunit Kv7.3


Mass: 96866.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ3 / Production host: Homo sapiens (human) / References: UniProt: O43525
#2: Protein Potassium voltage-gated channel subfamily KQT member 2 / KQT-like 2 / Neuroblastoma-specific potassium channel subunit alpha KvLQT2 / Voltage-gated ...KQT-like 2 / Neuroblastoma-specific potassium channel subunit alpha KvLQT2 / Voltage-gated potassium channel subunit Kv7.2


Mass: 95976.742 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ2 / Production host: Homo sapiens (human) / References: UniProt: O43526
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-A1EY8 / Azetukalner


Mass: 368.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H29FN2O / 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: KCNQ2/3 heteromeric complex with XEN1101 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: METHANE

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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: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189473 / Symmetry type: POINT
RefinementHighest resolution: 2.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028384
ELECTRON MICROSCOPYf_angle_d0.39411367
ELECTRON MICROSCOPYf_dihedral_angle_d3.9221191
ELECTRON MICROSCOPYf_chiral_restr0.0341247
ELECTRON MICROSCOPYf_plane_restr0.0051397

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