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- EMDB-66589: Cryo-EM structure of the human KCNQ2/3 heteromer channel -

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Basic information

Entry
Database: EMDB / ID: EMD-66589
TitleCryo-EM structure of the human KCNQ2/3 heteromer channel
Map data
Sample
  • Complex: Cryo-EM structure of the human KCNQ2/3 heteromer channel
    • Protein or peptide: Calmodulin-1
  • 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
KeywordsKv7 / Ion Channel / 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 / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Interaction between L1 and Ankyrins / Calmodulin induced events / ankyrin binding / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / voltage-gated monoatomic cation channel activity / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / neuron remodeling / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / : / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / exocytosis / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / regulation of cell communication by electrical coupling involved in cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / action potential / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / voltage-gated potassium channel activity / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / protein targeting / calcium channel inhibitor activity / presynaptic cytosol / neuronal action potential / Activation of AMPK downstream of NMDARs / cellular response to interferon-beta / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Protein methylation / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / potassium ion transmembrane transport / FCGR3A-mediated IL10 synthesis / regulation of heart rate / cellular response to calcium ion / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Ras activation upon Ca2+ influx through NMDA receptor / calyx of Held / adenylate cyclase activator activity / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / regulation of cytokinesis / protein serine/threonine kinase activator activity / spindle microtubule / sarcomere / positive regulation of receptor signaling pathway via JAK-STAT / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / Transcriptional activation of mitochondrial biogenesis / sensory perception of sound
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 / : / EF-hand domain pair ...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 / : / 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 / EF-hand domain pair / 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 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsCheng XY / Wan SY / Hou PP / Zhang J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of the human KCNQ2/3 heteromer channel
Authors: Cheng XY / Wan SY / Hou PP / Zhang J
History
DepositionOct 13, 2025-
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_66589.png

Downloads & links

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Map

FileDownload / File: emd_66589.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 356.4 Å		0.89 Å/pix.
x 400 pix.
= 356.4 Å		0.89 Å/pix.
x 400 pix.
= 356.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.891 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-2.0583236 - 3.0359862
Average (Standard dev.)-0.00023815337 (±0.04265909)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 356.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66589_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66589_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 : Cryo-EM structure of the human KCNQ2/3 heteromer channel

EntireName: Cryo-EM structure of the human KCNQ2/3 heteromer channel
Components
  • Complex: Cryo-EM structure of the human KCNQ2/3 heteromer channel
    • Protein or peptide: Calmodulin-1
  • 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

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Supramolecule #1: Cryo-EM structure of the human KCNQ2/3 heteromer channel

SupramoleculeName: Cryo-EM structure of the human KCNQ2/3 heteromer channel
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.164715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
TEEQIAEFKE AFSLFDKDGD GTITTKELGT VMRSLGQNPT EAELQDMINE VDADGNGTID FPEFLTMMAR KMKDTDSEEE IREAFRVFD KDGNGYISAA ELRHVMTNLG EKLTDEEVDE MIREADIDGD GQVNYEEFVQ MMTA

UniProtKB: Calmodulin-1

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Macromolecule #2: Potassium voltage-gated channel subfamily KQT member 3

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 3
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.968828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KYRRIQTLIY DALERPRGWA LLYHALVFLI VLGCLILAVL TTFKEYETVS GDWLLLLETF AIFIFGAEFA LRIWAAGCCC RYKGWRGRL KFARKPLCML DIFVLIASVP VVAVGNQGNV LATSLRSLRF LQILRMLRMD RRGGTWKLLG SAICAHSKEL I TAWYIGFL ...String:
KYRRIQTLIY DALERPRGWA LLYHALVFLI VLGCLILAVL TTFKEYETVS GDWLLLLETF AIFIFGAEFA LRIWAAGCCC RYKGWRGRL KFARKPLCML DIFVLIASVP VVAVGNQGNV LATSLRSLRF LQILRMLRMD RRGGTWKLLG SAICAHSKEL I TAWYIGFL TLILSSFLVY LVEKDVPEVD AQGEEMKEEF ETYADALWWG LITLATIGYG DKTPKTWEGR LIAATFSLIG VS FFALPAG ILGSGLALKV QEQHRQKHFE KRRKPAAELI QAAWRYYATN PNRIDLVATW RFYESVVSFP FFRKEQLEAA SSQ KLGLLD RVRLSNPRGS NTKGKLFTPL NVDAIEESPS KEPKPVGLNN KERFRTAFRM KAYAFWQSSE DAGTGDPMAE DRGY GNDFP IEDMIPTLKA AIRAVRILQF RLYKKKFKET LRPYDVKDVI EQYSAGHLDM LSRIKYLQTR IDMIFT

UniProtKB: Potassium voltage-gated channel subfamily KQT member 3

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Macromolecule #3: Potassium voltage-gated channel subfamily KQT member 2

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.18534 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RNAFYRKLQN FLYNVLERPR GWAFIYHAYV FLLVFSCLVL SVFSTIKEYE KSSEGALYIL EIVTIVVFGV EYFVRIWAAG CCCRYRGWR GRLKFARKPF CVIDIMVLIA SIAVLAAGSQ GNVFATSALR SLRFLQILRM IRMDRRGGTW KLLGSVVYAH S KELVTAWY ...String:
RNAFYRKLQN FLYNVLERPR GWAFIYHAYV FLLVFSCLVL SVFSTIKEYE KSSEGALYIL EIVTIVVFGV EYFVRIWAAG CCCRYRGWR GRLKFARKPF CVIDIMVLIA SIAVLAAGSQ GNVFATSALR SLRFLQILRM IRMDRRGGTW KLLGSVVYAH S KELVTAWY IGFLCLILAS FLVYLAEKGE NDHFDTYADA LWWGLITLTT IGYGDKYPQT WNGRLLAATF TLIGVSFFAL PA GILGSGF ALKVQEQHRQ KHFEKRRNPA AGLIQSAWRF YATNLSRTDL HSTWQYYERT VTVPMYSSQT QTYGASRLIP PLN QLELLR NLKSKSGLAF RKDPPPEPSP SKGSPCRGPL CGCCPGRSSQ KVSLKDRVFS SPRGVAAKGK GSPQAQTVRR SPSA DQSLE DSPSKVPKSW SFGDRSRARQ AFRIKGAASR QNSEEASLPG EDIVDDKSCP CEFVTEDLTP GLKVSIRAVC VMRFL VSKR KFKESLRPYD VMDVIEQYSA GHLDMLSRIK SLQSRVDQIV G

UniProtKB: Potassium voltage-gated channel subfamily KQT member 2

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Macromolecule #4: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 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: 50.44 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: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 217315
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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