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- EMDB-68147: XEN1101 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68147
TitleXEN1101 bound KCNQ2/3 heteromer with 3:1 stoichiometry, state 1
Map data
Sample
  • Complex: KCNQ2/3 heteromeric complex with XEN1101
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 2
  • Ligand: POTASSIUM ION
  • Ligand: Azetukalner
KeywordsM-channel / KCNQ2/3 / heteromeric channel / cryoEM / XEN1101 / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLu F / Fan X / Huang J
Funding support China, 1 items
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, 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_68147.png

Downloads & links

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Map

FileDownload / File: emd_68147.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 280 pix.
= 262.08 Å		0.94 Å/pix.
x 280 pix.
= 262.08 Å		0.94 Å/pix.
x 280 pix.
= 262.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.936 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.7359562 - 1.2008517
Average (Standard dev.)0.0012992079 (±0.025482977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 262.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68147_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_68147_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 : KCNQ2/3 heteromeric complex with XEN1101

EntireName: KCNQ2/3 heteromeric complex with XEN1101
Components
  • Complex: KCNQ2/3 heteromeric complex with XEN1101
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 2
  • Ligand: POTASSIUM ION
  • Ligand: Azetukalner

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Supramolecule #1: KCNQ2/3 heteromeric complex with XEN1101

SupramoleculeName: KCNQ2/3 heteromeric complex with XEN1101 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 1 / 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: Potassium voltage-gated channel subfamily KQT member 2

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 2
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.976742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG GAGAGKPPKR NAFYRKLQNF LYNVLERPR GWAFIYHAYV FLLVFSCLVL SVFSTIKEYE KSSEGALYIL EIVTIVVFGV EYFVRIWAAG CCCRYRGWRG R LKFARKPF ...String:
MVQKSRNGGV YPGPSGEKKL KVGFVGLDPG APDSTRDGAL LIAGSEAPKR GSILSKPRAG GAGAGKPPKR NAFYRKLQNF LYNVLERPR GWAFIYHAYV FLLVFSCLVL SVFSTIKEYE KSSEGALYIL EIVTIVVFGV EYFVRIWAAG CCCRYRGWRG R LKFARKPF CVIDIMVLIA SIAVLAAGSQ GNVFATSALR SLRFLQILRM IRMDRRGGTW KLLGSVVYAH SKELVTAWYI GF LCLILAS FLVYLAEKGE NDHFDTYADA LWWGLITLTT IGYGDKYPQT WNGRLLAATF TLIGVSFFAL PAGILGSGFA LKV QEQHRQ KHFEKRRNPA AGLIQSAWRF YATNLSRTDL HSTWQYYERT VTVPMYSSQT QTYGASRLIP PLNQLELLRN LKSK SGLAF RKDPPPEPSP SKGSPCRGPL CGCCPGRSSQ KVSLKDRVFS SPRGVAAKGK GSPQAQTVRR SPSADQSLED SPSKV PKSW SFGDRSRARQ AFRIKGAASR QNSEEASLPG EDIVDDKSCP CEFVTEDLTP GLKVSIRAVC VMRFLVSKRK FKESLR PYD VMDVIEQYSA GHLDMLSRIK SLQSRVDQIV GRGPAITDKD RTKGPAEAEL PEDPSMMGRL GKVEKQVLSM EKKLDFL VN IYMQRMGIPP TETEAYFGAK EPEPAPPYHS PEDSREHVDR HGCIVKIVRS SSSTGQKNFS APPAAPPVQC PPSTSWQP Q SHPRQGHGTS PVGDHGSLVR IPPPPAHERS LSAYGGGNRA SMEFLRQEDT PGCRPPEGNL RDSDTSISIP SVDHEELER SFSGFSISQS KENLDALNSC YAAVAPCAKV RPYIAEGESD TDSDLCTPCG PPPRSATGEG PFGDVGWAGP RK

UniProtKB: Potassium voltage-gated channel subfamily KQT member 2

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: Azetukalner

MacromoleculeName: Azetukalner / type: ligand / ID: 4 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 171895
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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