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Yorodumi- PDB-7tj9: Cryo-EM structure of the human Nax channel in complex with beta3 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tj9 | ||||||
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Title | Cryo-EM structure of the human Nax channel in complex with beta3 solved in GDN | ||||||
Components | (Sodium channel ...) x 2 | ||||||
Keywords | TRANSPORT PROTEIN / Sodium Channel / NaV / Ion Channel | ||||||
Function / homology | Function and homology information SA node cell action potential / regulation of ventricular cardiac muscle cell membrane depolarization / membrane depolarization during action potential / sodium ion homeostasis / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated monoatomic ion channel activity / voltage-gated sodium channel complex ...SA node cell action potential / regulation of ventricular cardiac muscle cell membrane depolarization / membrane depolarization during action potential / sodium ion homeostasis / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated monoatomic ion channel activity / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / cellular homeostasis / cardiac muscle cell action potential involved in contraction / ventricular cardiac muscle cell action potential / voltage-gated sodium channel activity / regulation of monoatomic ion transmembrane transport / sodium channel inhibitor activity / Interaction between L1 and Ankyrins / positive regulation of heart rate / sodium ion transport / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / glial cell projection / membrane depolarization / neuronal action potential / sodium ion transmembrane transport / sodium channel regulator activity / cardiac muscle contraction / muscle contraction / protein localization to plasma membrane / response to bacterium / Z disc / nervous system development / transmembrane transporter binding / axon / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Noland, C.L. / Kschonsak, M. / Ciferri, C. / Payandeh, J. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure-guided unlocking of Na reveals a non-selective tetrodotoxin-sensitive cation channel. Authors: Cameron L Noland / Han Chow Chua / Marc Kschonsak / Stephanie Andrea Heusser / Nina Braun / Timothy Chang / Christine Tam / Jia Tang / Christopher P Arthur / Claudio Ciferri / Stephan ...Authors: Cameron L Noland / Han Chow Chua / Marc Kschonsak / Stephanie Andrea Heusser / Nina Braun / Timothy Chang / Christine Tam / Jia Tang / Christopher P Arthur / Claudio Ciferri / Stephan Alexander Pless / Jian Payandeh / Abstract: Unlike classical voltage-gated sodium (Na) channels, Na has been characterized as a voltage-insensitive, tetrodotoxin-resistant, sodium (Na)-activated channel involved in regulating Na homeostasis. ...Unlike classical voltage-gated sodium (Na) channels, Na has been characterized as a voltage-insensitive, tetrodotoxin-resistant, sodium (Na)-activated channel involved in regulating Na homeostasis. However, Na remains refractory to functional characterization in traditional heterologous systems. Here, to gain insight into its atypical physiology, we determine structures of the human Na channel in complex with the auxiliary β3-subunit. Na reveals structural alterations within the selectivity filter, voltage sensor-like domains, and pore module. We do not identify an extracellular Na-sensor or any evidence for a Na-based activation mechanism in Na. Instead, the S6-gate remains closed, membrane lipids fill the central cavity, and the domain III-IV linker restricts S6-dilation. We use protein engineering to identify three pore-wetting mutations targeting the hydrophobic S6-gate that unlock a robust voltage-insensitive leak conductance. This constitutively active Na-QTT channel construct is non-selective among monovalent cations, inhibited by extracellular calcium, and sensitive to classical Na channel blockers, including tetrodotoxin. Our findings highlight a functional diversity across the Na channel scaffold, reshape our understanding of Na physiology, and provide a template to demystify recalcitrant ion channels. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tj9.cif.gz | 263.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tj9.ent.gz | 209.5 KB | Display | PDB format |
PDBx/mmJSON format | 7tj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/7tj9 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/7tj9 | HTTPS FTP |
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-Related structure data
Related structure data | 25920MC 7tj8C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Sodium channel ... , 2 types, 2 molecules AB
#1: Protein | Mass: 199684.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCN7A, SCN6A / Production host: Homo sapiens (human) / References: UniProt: Q01118 |
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#2: Protein | Mass: 24723.209 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCN3B, KIAA1158 / Production host: Homo sapiens (human) / References: UniProt: Q9NY72 |
-Sugars , 2 types, 6 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#7: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 17 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PLM / #8: Chemical | #9: Chemical | ChemComp-Q7G / | |
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-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: Complex between human Nax and the Beta3 auxiliary subunit Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 1.067 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1420422 / Symmetry type: POINT | ||||||||||||||||||||||||
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