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- EMDB-68620: Human KCNQ3-CaM in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-68620
TitleHuman KCNQ3-CaM in apo state
Map data
Sample
  • Complex: human KCNQ3-CaM in apo state
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Calmodulin-1
  • Ligand: POTASSIUM ION
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 / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Interaction between L1 and Ankyrins / Calmodulin induced events / 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 / 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 / RAF activation / response to calcium ion
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 / : / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...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 / : / 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 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 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-CaM in apo state
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_68620.png

Downloads & links

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Map

FileDownload / File: emd_68620.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.)X (Row.)Y (Col.)
0.93 Å/pix.
x 400 pix.
= 370.4 Å		0.93 Å/pix.
x 400 pix.
= 370.4 Å		0.93 Å/pix.
x 400 pix.
= 370.4 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-1.2969581 - 2.368359
Average (Standard dev.)0.0003038322 (±0.03414375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 370.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68620_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_68620_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-CaM in apo state

EntireName: human KCNQ3-CaM in apo state
Components
  • Complex: human KCNQ3-CaM in apo state
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Calmodulin-1
  • Ligand: POTASSIUM ION

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Supramolecule #1: human KCNQ3-CaM in apo state

SupramoleculeName: human KCNQ3-CaM in apo state / 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: 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: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / 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: 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: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 76016
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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