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- EMDB-61109: human KCNQ5-CaM in apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-61109
Titlehuman KCNQ5-CaM in apo state
Map data
Sample
  • Complex: human KCNQ5-CaM in apo state
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 5
    • Protein or peptide: Calmodulin-1
Keywordsvoltage-gated potassium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


clathrin coat / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Voltage gated Potassium channels / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...clathrin coat / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Voltage gated Potassium channels / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / 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 / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / 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 / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / voltage-gated potassium channel activity / detection of calcium ion / catalytic complex / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / cellular response to interferon-beta / Protein methylation / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / VEGFR2 mediated cell proliferation / protein serine/threonine kinase activator activity / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / cellular response to type II interferon / Stimuli-sensing channels / G2/M transition of mitotic cell cycle / long-term synaptic potentiation / spindle pole / RAS processing / calcium-dependent protein binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / Platelet degranulation / Inactivation, recovery and regulation of the phototransduction cascade / myelin sheath / presynaptic membrane / RAF/MAP kinase cascade / Ca2+ pathway
Similarity search - Function
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 ...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
Calmodulin-1 / Potassium voltage-gated channel subfamily KQT member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsYang Z / Guo J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32371204 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Phosphatidylinositol 4,5-bisphosphate activation mechanism of human KCNQ5.
Authors: Zhenni Yang / Yueming Zheng / Demin Ma / Long Wang / Jiatong Zhang / Tiefeng Song / Yong Wang / Yan Zhang / Fajun Nan / Nannan Su / Zhaobing Gao / Jiangtao Guo /
Abstract: The human voltage-gated potassium channels KCNQ2, KCNQ3, and KCNQ5 can form homo- and heterotetrameric channels that are responsible for generating the neuronal M current and maintaining the membrane ...The human voltage-gated potassium channels KCNQ2, KCNQ3, and KCNQ5 can form homo- and heterotetrameric channels that are responsible for generating the neuronal M current and maintaining the membrane potential stable. Activation of KCNQ channels requires both the depolarization of membrane potential and phosphatidylinositol 4,5-bisphosphate (PIP). Here, we report cryoelectron microscopy structures of the human KCNQ5-calmodulin (CaM) complex in the apo, PIP-bound, and both PIP- and the activator HN37-bound states in either a closed or an open conformation. In the closed conformation, a PIP molecule binds in the middle of the groove between two adjacent voltage-sensing domains (VSDs), whereas in the open conformation, one additional PIP binds to the interface of VSD and the pore domain, accompanying structural rearrangement of the cytosolic domain of KCNQ and CaM. The structures, along with electrophysiology analyses, reveal the two different binding modes of PIP and elucidate the PIP activation mechanism of KCNQ5.
History
DepositionAug 8, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61109.png

Downloads & links

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Map

FileDownload / File: emd_61109.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.04420542 - 0.12524247
Average (Standard dev.)0.000059600792 (±0.0025836923)
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: #1

Fileemd_61109_half_map_1.map
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Half map: #2

Fileemd_61109_half_map_2.map
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Sample components

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Entire : human KCNQ5-CaM in apo state

EntireName: human KCNQ5-CaM in apo state
Components
  • Complex: human KCNQ5-CaM in apo state
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 5
    • Protein or peptide: Calmodulin-1

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Supramolecule #1: human KCNQ5-CaM in apo state

SupramoleculeName: human KCNQ5-CaM in apo state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Potassium voltage-gated channel subfamily KQT member 5

MacromoleculeName: Potassium voltage-gated channel subfamily KQT member 5
type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.776484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLGKPLSYTS SQSCRRNVKY RRVQNYLYNV LERPRGWAFI YHAFVFLLVF GCLILSVFST IPEHTKLASS CLLILEFVMI VVFGLEFII RIWSAGCCCR YRGWQGRLRF ARKPFCVIDT IVLIASIAVV SAKTQGNIFA TSALRSLRFL QILRMVRMDR R GGTWKLLG ...String:
MLGKPLSYTS SQSCRRNVKY RRVQNYLYNV LERPRGWAFI YHAFVFLLVF GCLILSVFST IPEHTKLASS CLLILEFVMI VVFGLEFII RIWSAGCCCR YRGWQGRLRF ARKPFCVIDT IVLIASIAVV SAKTQGNIFA TSALRSLRFL QILRMVRMDR R GGTWKLLG SVVYAHSKEL ITAWYIGFLV LIFSSFLVYL VEKDANKEFS TYADALWWGT ITLTTIGYGD KTPLTWLGRL LS AGFALLG ISFFALPAGI LGSGFALKVQ EQHRQKHFEK RRNPAANLIQ CVWRSYAADE KSVSIATWKP HLKALHTCSP TKK EQGEAS SSQKLSFKER VRMASPRGQS IKSRQASVGD RRSPSTDITA EGSPTKVQKS WSFNDRTRFR PSLRLKSSQP KPVI DADTA LGTDDVYDEK GCQCDVSVED LTPPLKTVIR AIRIMKFHVA KRKFKETLRP YDVKDVIEQY SAGHLDMLCR IKSLQ TRVD QILGKGQITS DKKSREKITA EHETTDDLSM LGRVVKVEKQ VQSIESKLDC LLDIYQQVLR KGSASALALA SFQIPP FEC EQTSDYQSPV DSKDLSGSAQ NSGCLSRSTS ANISRGLQFI LTPNEFS

UniProtKB: Potassium voltage-gated channel subfamily KQT member 5

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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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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (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 / Cs: 2.7 mm / 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 314095
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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