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- PDB-9lj1: Human KCNQ5-CaM-PIP2-HN37 complex in a closed conformation. -

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Basic information

Entry
Database: PDB / ID: 9lj1
TitleHuman KCNQ5-CaM-PIP2-HN37 complex in a closed conformation.
Components
  • Calmodulin-3
  • Potassium voltage-gated channel subfamily KQT member 5
KeywordsMEMBRANE PROTEIN / voltage-gated potassium channel
Function / homology
Function and homology information


clathrin coat / transporter inhibitor activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Voltage gated Potassium channels / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential ...clathrin coat / transporter inhibitor activity / voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / Voltage gated Potassium channels / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / negative regulation of high voltage-gated calcium channel activity / response to corticosterone / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / calcineurin-mediated signaling / protein phosphatase activator activity / adenylate cyclase binding / catalytic complex / regulation of synaptic vesicle endocytosis / voltage-gated potassium channel activity / detection of calcium ion / regulation of cardiac muscle contraction / postsynaptic cytosol / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / phosphatidylinositol 3-kinase binding / presynaptic cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / potassium ion transmembrane transport / calcium channel complex / substantia nigra development / regulation of heart rate / calyx of Held / adenylate cyclase activator activity / response to amphetamine / sarcomere / regulation of cytokinesis / protein serine/threonine kinase activator activity / nitric-oxide synthase regulator activity / spindle microtubule / calcium channel regulator activity / response to calcium ion / mitochondrial membrane / G2/M transition of mitotic cell cycle / Schaffer collateral - CA1 synapse / long-term synaptic potentiation / spindle pole / calcium-dependent protein binding / synaptic vesicle membrane / myelin sheath / growth cone / presynaptic membrane / vesicle / transmembrane transporter binding / G protein-coupled receptor signaling pathway / protein domain specific binding / calcium ion binding / centrosome / protein kinase binding / protein-containing complex / nucleus / plasma membrane / cytoplasm
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
Chem-9MF / Chem-PIO / Calmodulin-3 / Potassium voltage-gated channel subfamily KQT member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYang, Z. / Guo, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870724 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
DepositionJan 14, 2025Deposition 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
E: Calmodulin-3
B: Potassium voltage-gated channel subfamily KQT member 5
C: Calmodulin-3
D: Potassium voltage-gated channel subfamily KQT member 5
F: Calmodulin-3
G: Potassium voltage-gated channel subfamily KQT member 5
H: Calmodulin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,66316
Polymers360,3158
Non-polymers4,3488
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: 70463.289 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-3


Mass: 19615.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM3, CALML2, CAM3, CAMC, CAMIII / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P0DP25
#3: Chemical
ChemComp-9MF / methyl N-[4-[(4-fluorophenyl)methyl-prop-2-ynyl-amino]-2,6-dimethyl-phenyl]carbamate / HN37


Mass: 340.391 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H21FN2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
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 / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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-PIP2-HN37 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: hek 293
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: TFS 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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90473 / Symmetry type: POINT

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