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- EMDB-66607: Cryo-EM structure of the human KCNQ2/3 heteromer channel in the X... -

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Basic information

Entry
Database: EMDB / ID: EMD-66607
TitleCryo-EM structure of the human KCNQ2/3 heteromer channel in the XEN1101-bound open state
Map data
Sample
  • Complex: Cryo-EM structure of the human KCNQ2/3 heteromer channel in the XEN1101-bound open state
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 2
    • Protein or peptide: Calmodulin-1
  • Ligand: Azetukalner
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: POTASSIUM ION
KeywordsKv7 / Ion Channel / 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 ...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 / Interaction between L1 and Ankyrins / Cam-PDE 1 activation / ankyrin binding / Sodium/Calcium exchangers / Calmodulin induced events / voltage-gated monoatomic cation channel activity / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / 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 / neuron remodeling / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / : / 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 / Protein methylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / 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 / potassium ion transmembrane transport / substantia nigra development / FCGR3A-mediated IL10 synthesis / cellular response to calcium ion / regulation of heart rate / 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
Similarity search - Function
Potassium channel, voltage dependent, KCNQ3 / 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 / : / EF-hand domain pair ...Potassium channel, voltage dependent, KCNQ3 / 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 / : / 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 / Ion transport domain / Ion transport protein / EF-hand domain pair
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: 3.19 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 in the XEN1101-bound open state
Authors: Cheng XY / Wan SY / Hou PP / Zhang J
History
DepositionOct 14, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66607.png

Downloads & links

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Map

FileDownload / File: emd_66607.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: 0.25
Minimum - Maximum-1.7639173 - 2.9675643
Average (Standard dev.)0.00044150784 (±0.040390477)
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_66607_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_66607_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 in the X...

EntireName: Cryo-EM structure of the human KCNQ2/3 heteromer channel in the XEN1101-bound open state
Components
  • Complex: Cryo-EM structure of the human KCNQ2/3 heteromer channel in the XEN1101-bound open state
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 3
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 2
    • Protein or peptide: Calmodulin-1
  • Ligand: Azetukalner
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: POTASSIUM ION

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

SupramoleculeName: Cryo-EM structure of the human KCNQ2/3 heteromer channel in the XEN1101-bound open state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #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: 16.852545 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 #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: 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 #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: 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 #4: Azetukalner

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

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Macromolecule #5: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 5 / Number of copies: 4 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Macromolecule #6: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 3 / 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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 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: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 131114
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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