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Yorodumi- PDB-7sx4: Human NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sx4 | ||||||
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Title | Human NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conformation 2/2 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / ion channel / calmodulin / HEAT repeat protein | ||||||
Function / homology | Function and homology information monoatomic cation homeostasis / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / cation channel complex / sodium channel activity / voltage-gated sodium channel activity / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers ...monoatomic cation homeostasis / positive regulation of synaptic transmission, cholinergic / leak channel activity / regulation of resting membrane potential / cation channel complex / sodium channel activity / voltage-gated sodium channel activity / 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 / negative regulation of high voltage-gated calcium channel activity / monoatomic ion channel complex / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / negative regulation of calcium ion export across plasma membrane / organelle localization by membrane tethering / Activation of RAC1 downstream of NMDARs / regulation of cardiac muscle cell action potential / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / negative regulation of peptidyl-threonine phosphorylation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / calcium ion import across plasma membrane / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Long-term potentiation / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / sodium ion transmembrane transport / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / Activation of AMPK downstream of NMDARs / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / monoatomic cation channel activity / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Ion homeostasis / positive regulation of protein autophosphorylation / potassium ion transmembrane transport / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / monoatomic ion transmembrane transport / protein serine/threonine kinase activator activity / bioluminescence / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / generation of precursor metabolites and energy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / positive regulation of synaptic transmission, GABAergic / calcium ion transmembrane transport / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / spindle pole / cellular response to type II interferon / response to calcium ion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Kschonsak, M. / Chua, H.C. / Weidling, C. / Chakouri, N. / Noland, C.L. / Schott, K. / Chang, T. / Tam, C. / Patel, N. / Arthur, C.P. ...Kschonsak, M. / Chua, H.C. / Weidling, C. / Chakouri, N. / Noland, C.L. / Schott, K. / Chang, T. / Tam, C. / Patel, N. / Arthur, C.P. / Leitner, A. / Ben-Johny, M. / Ciferri, C. / Pless, S.A. / Payandeh, J. | ||||||
Funding support | 1items
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Citation | Journal: Nature / Year: 2022 Title: Structural architecture of the human NALCN channelosome. Authors: Marc Kschonsak / Han Chow Chua / Claudia Weidling / Nourdine Chakouri / Cameron L Noland / Katharina Schott / Timothy Chang / Christine Tam / Nidhi Patel / Christopher P Arthur / Alexander ...Authors: Marc Kschonsak / Han Chow Chua / Claudia Weidling / Nourdine Chakouri / Cameron L Noland / Katharina Schott / Timothy Chang / Christine Tam / Nidhi Patel / Christopher P Arthur / Alexander Leitner / Manu Ben-Johny / Claudio Ciferri / Stephan Alexander Pless / Jian Payandeh / Abstract: Depolarizing sodium (Na) leak currents carried by the NALCN channel regulate the resting membrane potential of many neurons to modulate respiration, circadian rhythm, locomotion and pain sensitivity. ...Depolarizing sodium (Na) leak currents carried by the NALCN channel regulate the resting membrane potential of many neurons to modulate respiration, circadian rhythm, locomotion and pain sensitivity. NALCN requires FAM155A, UNC79 and UNC80 to function, but the role of these auxiliary subunits is not understood. NALCN, UNC79 and UNC80 are essential in rodents, and mutations in human NALCN and UNC80 cause severe developmental and neurological disease. Here we determined the structure of the NALCN channelosome, an approximately 1-MDa complex, as fundamental aspects about the composition, assembly and gating of this channelosome remain obscure. UNC79 and UNC80 are massive HEAT-repeat proteins that form an intertwined anti-parallel superhelical assembly, which docks intracellularly onto the NALCN-FAM155A pore-forming subcomplex. Calmodulin copurifies bound to the carboxy-terminal domain of NALCN, identifying this region as a putative modulatory hub. Single-channel analyses uncovered a low open probability for the wild-type complex, highlighting the tightly closed S6 gate in the structure, and providing a basis to interpret the altered gating properties of disease-causing variants. Key constraints between the UNC79-UNC80 subcomplex and the NALCN DI-DII and DII-DIII linkers were identified, leading to a model of channelosome gating. Our results provide a structural blueprint to understand the physiology of the NALCN channelosome and a template for drug discovery to modulate the resting membrane potential. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7sx4.cif.gz | 897 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sx4.ent.gz | 701.1 KB | Display | PDB format |
PDBx/mmJSON format | 7sx4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/7sx4 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/7sx4 | HTTPS FTP |
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-Related structure data
Related structure data | 25493MC 7sx3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 234128.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NALCN, VGCNL1, eGFP / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8IZF0, UniProt: A0A7G8ZY66 |
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#2: Protein | Mass: 54205.004 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FAM155A / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: B1AL88 |
#3: Protein | Mass: 16852.545 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P0DP23 |
#4: Protein | Mass: 285174.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UNC79, UNC79, KIAA1409 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q9P2D8 |
#5: Protein | Mass: 366510.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UNC80, C2orf21, KIAA1843 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8N2C7 |
-Sugars , 1 types, 2 molecules
#6: Sugar |
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-Non-polymers , 3 types, 5 molecules
#7: Chemical | ChemComp-PEV / ( |
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#8: Chemical | ChemComp-PGV / ( |
#9: Chemical |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pentameric complex of the leak channel NALCN with FAM155A, Calmodulin, UNC79 and UNC80 Type: COMPLEX Details: Calmodulin was not overexpressed but co-purified from Expi293 cells Entity ID: #1-#5 / Source: RECOMBINANT | |||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Strain: Expi293 | |||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.65 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: NALCN was reconstituted into lipid nanodiscs and mildly crosslinkned with 0.05% EM grade glutaraldehyde for 10 min at room temperature. Cross-linking was quenched with 9 mM Tris pH 7.5 | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0.6/1 | |||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3.5 sec blotting |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 64.009 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 26550 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Details: selected micrographs with a CTF fit of 10.0 A or better Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3048401 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56037 / Num. of class averages: 1 / Symmetry type: POINT |