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Yorodumi- EMDB-25492: Human NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conf... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25492 | |||||||||
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Title | Human NALCN-FAM155A-UNC79-UNC80 channelosome with CaM bound, conformation 1/2 | |||||||||
Map data | combined map of focused refinements used for model refinements | |||||||||
Sample |
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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 | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Kschonsak M / Chua HC / Weidling C / Chakouri N / Noland CL / Schott K / Chang T / Tam C / Patel N / Arthur CP ...Kschonsak M / Chua HC / Weidling C / Chakouri N / Noland CL / Schott K / Chang T / Tam C / Patel N / Arthur CP / Leitner A / Ben-Johny M / Ciferri C / Pless SA / Payandeh J | |||||||||
Funding support | 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25492.map.gz | 221.2 MB | EMDB map data format | |
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Header (meta data) | emd-25492-v30.xml emd-25492.xml | 69.4 KB 69.4 KB | Display Display | EMDB header |
Images | emd_25492.png | 90.3 KB | ||
Others | emd_25492_additional_1.map.gz emd_25492_additional_10.map.gz emd_25492_additional_11.map.gz emd_25492_additional_12.map.gz emd_25492_additional_13.map.gz emd_25492_additional_14.map.gz emd_25492_additional_15.map.gz emd_25492_additional_16.map.gz emd_25492_additional_17.map.gz emd_25492_additional_2.map.gz emd_25492_additional_3.map.gz emd_25492_additional_4.map.gz emd_25492_additional_5.map.gz emd_25492_additional_6.map.gz emd_25492_additional_7.map.gz emd_25492_additional_8.map.gz emd_25492_additional_9.map.gz emd_25492_half_map_1.map.gz emd_25492_half_map_2.map.gz | 226.1 MB 89.6 MB 89.6 MB 226.9 MB 225.9 MB 89.6 MB 89.6 MB 226.9 MB 89.6 MB 89.6 MB 226.1 MB 226.8 MB 226 MB 89.6 MB 89.6 MB 226.5 MB 226.2 MB 89.6 MB 89.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25492 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25492 | HTTPS FTP |
-Related structure data
Related structure data | 7sx3MC 7sx4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25492.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | combined map of focused refinements used for model refinements | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1732 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Additional map: map (non-sharpened) of focused NALCN-FAM region containing the...
+Additional map: halfmap 2 of focused UNC-crossover region containing the...
+Additional map: halfmap 1 of focused UNC-crossover region containing the...
+Additional map: sharpened map of focused UNC-CN region containing the...
+Additional map: map (non-sharpened) of focused UNC-CN region containing the...
+Additional map: halfmap 2 of focused UNC-CN region containing the...
+Additional map: halfmap 1 of focused UNC-CN region containing the...
+Additional map: sharpened map of focused NALCN-FAM region containing the...
+Additional map: halfmap 1 of focused NALCN-FAM region containing the...
+Additional map: halfmap 2 of focused NALCN-FAM region containing the...
+Additional map: map (non-sharpened) of overall NALCN-FAM-UNC79-UNC80-CAM used for alignment...
+Additional map: sharpened map of focused UNC-NC region containing the...
+Additional map: map (non-sharpened) of focused UNC-NC region containing the...
+Additional map: halfmap 2 of focused UNC-NC region containing the...
+Additional map: halfmap 1 of focused UNC-NC region containing the...
+Additional map: sharpened map of focused UNC-crossover region containing the...
+Additional map: map (non-sharpened) of focused UNC-crossover region containing the...
+Half map: halfmap 1 (non-sharpened) of overall NALCN-FAM-UNC79-UNC80-CAM
+Half map: halfmap 2 (non-sharpened) of overall NALCN-FAM-UNC79-UNC80-CAM
-Sample components
+Entire : Pentameric complex of the leak channel NALCN with FAM155A, Calmod...
+Supramolecule #1: Pentameric complex of the leak channel NALCN with FAM155A, Calmod...
+Macromolecule #1: Sodium leak channel non-selective protein,Enhanced green fluoresc...
+Macromolecule #2: Transmembrane protein FAM155A
+Macromolecule #3: Calmodulin-1
+Macromolecule #4: UNC79,Protein unc-79 homolog,Protein unc-79 homolog
+Macromolecule #5: Protein unc-80 homolog
+Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
+Macromolecule #7: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...
+Macromolecule #8: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...
+Macromolecule #9: CHOLESTEROL HEMISUCCINATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.65 mg/mL | |||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: UltrAuFoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP / Details: 3.5 sec blotting. | |||||||||
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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 26550 / Average exposure time: 3.0 sec. / Average electron dose: 64.009 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 3048401 |
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CTF correction | Software - Name: CTFFIND (ver. 4.1.13) Details: selected micrographs with a CTF fit of 10.0 A or better |
Startup model | Type of model: OTHER / Details: ab initio 3D reconstruction within cisTEM |
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cisTEM (ver. 1.02) |
Final 3D classification | Number classes: 8 / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: OTHER / Software - Name: cisTEM (ver. 1.02) Details: Focused refinements were conducted after dividing the map into four distinct regions. |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.02) / Number images used: 132257 |