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- PDB-9j38: human KCNQ5-CaM in apo state -

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Basic information

Entry
Database: PDB / ID: 9j38
Titlehuman KCNQ5-CaM in apo state
Components
  • Calmodulin-1
  • Potassium voltage-gated channel subfamily KQT member 5
KeywordsMEMBRANE PROTEIN / voltage-gated potassium channel
Function / homology
Function and homology information


clathrin coat / 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 ...clathrin coat / 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 / PKA activation / CaMK IV-mediated phosphorylation of CREB / CASP4 inflammasome assembly / Glycogen breakdown (glycogenolysis) / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / negative regulation of high voltage-gated calcium channel activity / 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 / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / regulation of cell communication by electrical coupling involved in cardiac conduction / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Regulation of MECP2 expression and activity / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / voltage-gated potassium channel activity / cellular response to interferon-beta / RHO GTPases activate IQGAPs / presynaptic cytosol / calcium channel inhibitor activity / catalytic complex / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of heart rate / Protein methylation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / titin binding / calcium channel complex / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / potassium ion transmembrane transport / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of receptor signaling pathway via JAK-STAT / calyx of Held / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / regulation of cytokinesis / VEGFR2 mediated cell proliferation / spindle microtubule / VEGFR2 mediated vascular permeability / calcium channel regulator activity / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / myelin sheath / Transcriptional activation of mitochondrial biogenesis / long-term synaptic potentiation / cellular response to type II interferon / Enterobacterial factors antagonize host defense / RAF activation / response to calcium ion / Stimuli-sensing channels / 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 / RAS processing / Signaling by BRAF and RAF1 fusions / Platelet degranulation / Inactivation, recovery and regulation of the phototransduction cascade / RAF/MAP kinase cascade / spindle pole / Ca2+ pathway / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / vesicle
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsYang, Z. / Guo, J.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potassium voltage-gated channel subfamily KQT member 5
B: Potassium voltage-gated channel subfamily KQT member 5
C: Potassium voltage-gated channel subfamily KQT member 5
D: Potassium voltage-gated channel subfamily KQT member 5
E: Calmodulin-1
F: Calmodulin-1
G: Calmodulin-1
H: Calmodulin-1


Theoretical massNumber of molelcules
Total (without water)342,5168
Polymers342,5168
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Potassium voltage-gated channel subfamily KQT member 5 / KQT-like 5 / Potassium channel subunit alpha KvLQT5 / Voltage-gated potassium channel subunit Kv7.5


Mass: 68776.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCNQ5 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NR82
#2: Protein
Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DP23
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human KCNQ5-CaM in apo state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Hek293
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 314095 / Symmetry type: POINT

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