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- EMDB-68626: Human KCNQ3-XEN1101 complex in the presence of PIP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-68626
TitleHuman KCNQ3-XEN1101 complex in the presence of PIP2
Map data
Sample
  • Complex: Human KCNQ3-XEN1101 complex in the presence of PIP2
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
  • Ligand: Azetukalner
KeywordsION CHANNEL / KCNQ3 / MEMBRANE PROTEIN
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 / voltage-gated monoatomic cation channel activity / neuron remodeling / exocytosis / 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 / neuron apoptotic process / gene expression / chemical synaptic transmission / calmodulin binding / synapse / cell surface / mitochondrion / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, KCNQ3 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsCheng XY / Wan SY / Jiang DX / Zhang HY / Hu B / Hou PP / Zhang J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271260 China
CitationJournal: To Be Published
Title: Human KCNQ3-XEN1101 complex in the presence of PIP2
Authors: Cheng XY / Wan SY / Jiang DX / Zhang HY / Hu B / Hou PP / Zhang J
History
DepositionJan 21, 2026-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68626.png

Downloads & links

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Map

FileDownload / File: emd_68626.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 322.8 Å		0.81 Å/pix.
x 400 pix.
= 322.8 Å		0.81 Å/pix.
x 400 pix.
= 322.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.807 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.3942889 - 2.2144802
Average (Standard dev.)-0.00041269645 (±0.029975038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 322.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68626_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68626_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human KCNQ3-XEN1101 complex in the presence of PIP2

EntireName: Human KCNQ3-XEN1101 complex in the presence of PIP2
Components
  • Complex: Human KCNQ3-XEN1101 complex in the presence of PIP2
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
  • Ligand: Azetukalner

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Supramolecule #1: Human KCNQ3-XEN1101 complex in the presence of PIP2

SupramoleculeName: Human KCNQ3-XEN1101 complex in the presence of PIP2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium voltage-gated channel subfamily KQT member 3

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 3
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.866391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGLKARRAAG AAGGGGDGGG GGGGAANPAG GDAAAAGDEE RKVGLAPGDV EQVTLALGAG ADKDGTLLLE GGGRDEGQRR TPQGIGLLA KTPLSRPVKR NNAKYRRIQT LIYDALERPR GWALLYHALV FLIVLGCLIL AVLTTFKEYE TVSGDWLLLL E TFAIFIFG ...String:
MGLKARRAAG AAGGGGDGGG GGGGAANPAG GDAAAAGDEE RKVGLAPGDV EQVTLALGAG ADKDGTLLLE GGGRDEGQRR TPQGIGLLA KTPLSRPVKR NNAKYRRIQT LIYDALERPR GWALLYHALV FLIVLGCLIL AVLTTFKEYE TVSGDWLLLL E TFAIFIFG AEFALRIWAA GCCCRYKGWR GRLKFARKPL CMLDIFVLIA SVPVVAVGNQ GNVLATSLRS LRFLQILRML RM DRRGGTW KLLGSAICAH SKELITAWYI GFLTLILSSF LVYLVEKDVP EVDAQGEEMK EEFETYADAL WWGLITLATI GYG DKTPKT WEGRLIAATF SLIGVSFFAL PAGILGSGLA LKVQEQHRQK HFEKRRKPAA ELIQAAWRYY ATNPNRIDLV ATWR FYESV VSFPFFRKEQ LEAASSQKLG LLDRVRLSNP RGSNTKGKLF TPLNVDAIEE SPSKEPKPVG LNNKERFRTA FRMKA YAFW QSSEDAGTGD PMAEDRGYGN DFPIEDMIPT LKAAIRAVRI LQFRLYKKKF KETLRPYDVK DVIEQYSAGH LDMLSR IKY LQTRIDMIFT PGPPSTPKHK KSQKGSAFTF PSQQSPRNEP YVARPSTSEI EDQSMMGKFV KVERQVQDMG KKLDFLV DM HMQHMERLQV QVTEYYPTKG TSSPAEAEKK EDNRYSDLKT IICNYSETGP PEPPYSFHQV TIDKVSPYGF FAHDPVNL P RGGPSSGKVQ ATPPSSATTY VERPTVLPIL TLLDSRVSCH SQADLQGPYS DRISPRQRRS ITRDSDTPLS LMSVNHEEL ERSPSGFSIS QDRDDYVFGP NGGSSWMREK RYLAEGETDT DTDPFTPSGS MPLSSTGDGI SDSVWTPSNK PI

UniProtKB: Potassium voltage-gated channel subfamily KQT member 3

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Macromolecule #2: Azetukalner

MacromoleculeName: Azetukalner / type: ligand / ID: 2 / Number of copies: 4 / Formula: A1EY8
Molecular weightTheoretical: 368.488 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.79 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: 1.0 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 78984
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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