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- EMDB-62892: Human KCNQ2-CaM in complex with QO-58 -

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Basic information

Entry
Database: EMDB / ID: EMD-62892
TitleHuman KCNQ2-CaM in complex with QO-58
Map data
Sample
  • Complex: Human KCNQ2-CaM in complex with QO-58
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 2
  • Ligand: QO-58
KeywordsKCNQ2 / membrane protein
Function / homology
Function and homology information


axon initial segment / Voltage gated Potassium channels / node of Ranvier / Interaction between L1 and Ankyrins / voltage-gated monoatomic cation channel activity / ankyrin binding / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport ...axon initial segment / Voltage gated Potassium channels / node of Ranvier / Interaction between L1 and Ankyrins / voltage-gated monoatomic cation channel activity / ankyrin binding / action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / potassium ion transmembrane transport / nervous system development / chemical synaptic transmission / calmodulin binding / synapse / membrane / plasma membrane
Similarity search - Function
Potassium channel, voltage dependent, KCNQ2 / Ankyrin-G binding site / Ankyrin-G binding motif of KCNQ2-3 / Unstructured region on Potassium channel subunit alpha KvLQT2 / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhao YW / Yang ZN / Du XN / Guo JT
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U21A20359 China
CitationJournal: Cell Rep / Year: 2025
Title: Structure basis for the activation of KCNQ2 by endogenous and exogenous ligands.
Authors: Yiwen Zhao / Zhenni Yang / Sai Shi / Han Hao / Xinmeng Li / Demin Ma / Nannan Su / Weixin Zhao / Jicheng Shao / Yating An / Ke Wang / Yinuo Liu / Lu Zou / Jinlong Qi / Hailin Zhang / Jiangtao Guo / Xiaona Du /
Abstract: The voltage-gated potassium channel KCNQ2 is crucial for stabilizing neuronal membrane potential, and its mutations can cause various epilepsies. KCNQ2 is activated by endogenous ligand ...The voltage-gated potassium channel KCNQ2 is crucial for stabilizing neuronal membrane potential, and its mutations can cause various epilepsies. KCNQ2 is activated by endogenous ligand phosphatidylinositol-4,5-bisphosphate (PIP) and exogenous ligands, yet the structural mechanisms underlying these activations remain unclear. Here, we report the cryo-electron microscopy structures of human KCNQ2 in complex with exogenous ligands QO-58 and QO-83 in the absence or presence of PIP in either closed or open conformation. While QO-83 binds in the classical fenestration pocket of the pore domain, QO-58 mainly binds at the flank of S4 in the voltage-sensing domain. These structures, along with electrophysiological assays and computational studies, provide mechanistic insights into the ligand activation of KCNQ2 and may guide the development of anti-epileptic drugs targeting KCNQ2.
History
DepositionDec 28, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62892.png

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Map

FileDownload / File: emd_62892.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å		0.93 Å/pix.
x 240 pix.
= 223.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0126
Minimum - Maximum-0.02806731 - 0.065768056
Average (Standard dev.)0.000054500146 (±0.0023854706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 223.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62892_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_62892_half_map_2.map
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Sample components

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Entire : Human KCNQ2-CaM in complex with QO-58

EntireName: Human KCNQ2-CaM in complex with QO-58
Components
  • Complex: Human KCNQ2-CaM in complex with QO-58
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 2
  • Ligand: QO-58

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Supramolecule #1: Human KCNQ2-CaM in complex with QO-58

SupramoleculeName: Human KCNQ2-CaM in complex with QO-58 / 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 2

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 2
type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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 #2: QO-58

MacromoleculeName: QO-58 / type: ligand / ID: 2 / Number of copies: 8 / Formula: A1LVR
Molecular weightTheoretical: 443.182 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.0 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: 0.8 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: PDB ENTRY
PDB model - PDB ID:

7cr3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103232
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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