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- EMDB-63128: Human KCNQ5-CaM in complex with PIP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-63128
TitleHuman KCNQ5-CaM in complex with PIP2
Map data
Sample
  • Complex: KCNQ5-CaM complex in the presence of PIP2
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 5
    • Protein or peptide: Calmodulin-3
  • 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
Keywordsvoltage-gated potassium channel / MEMBRANE PROTEIN
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 / response to corticosterone / negative regulation of high voltage-gated calcium channel activity / 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 / response to corticosterone / negative regulation of high voltage-gated calcium channel activity / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / nitric-oxide synthase binding / regulation of synaptic vesicle exocytosis / regulation of cell communication by electrical coupling involved in cardiac conduction / calcineurin-mediated signaling / adenylate cyclase binding / protein phosphatase activator activity / voltage-gated potassium channel activity / catalytic complex / detection of calcium ion / regulation of synaptic vesicle endocytosis / 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 / response to amphetamine / adenylate cyclase activator activity / sarcomere / nitric-oxide synthase regulator activity / protein serine/threonine kinase activator activity / regulation of cytokinesis / 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 / presynaptic membrane / growth cone / 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
Calmodulin-3 / Potassium voltage-gated channel subfamily KQT member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYang Z / Guo J
Funding support China, 1 items
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, 2025-
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_63128.png

Downloads & links

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Map

FileDownload / File: emd_63128.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: 0.005
Minimum - Maximum-0.057225958 - 0.09092765
Average (Standard dev.)0.00008588711 (±0.002584329)
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: #2

Fileemd_63128_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63128_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : KCNQ5-CaM complex in the presence of PIP2

EntireName: KCNQ5-CaM complex in the presence of PIP2
Components
  • Complex: KCNQ5-CaM complex in the presence of PIP2
    • Protein or peptide: Potassium voltage-gated channel subfamily KQT member 5
    • Protein or peptide: Calmodulin-3
  • 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

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Supramolecule #1: KCNQ5-CaM complex in the presence of PIP2

SupramoleculeName: KCNQ5-CaM complex in the presence of PIP2 / 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 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: 70.463289 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 LTPNEFSLEG GSSGGWSHPQ FEK

UniProtKB: Potassium voltage-gated channel subfamily KQT member 5

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Macromolecule #2: Calmodulin-3

MacromoleculeName: Calmodulin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.615445 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK LEGGSSGGLV P RGSGGSSG GHHHHHHHH

UniProtKB: Calmodulin-3

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Macromolecule #3: [(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: 3 / 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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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

MicroscopeTFS 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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