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Open data
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Basic information
Entry | Database: PDB / ID: 7xsu | ||||||
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Title | Cardiac sodium channel in complex with LqhIII | ||||||
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![]() | MEMBRANE PROTEIN/TOXIN / cardiac sodium channel / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TOXIN complex | ||||||
Function / homology | ![]() voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / sodium channel complex / SA node cell action potential / AV node cell to bundle of His cell communication / membrane depolarization during SA node cell action potential / response to denervation involved in regulation of muscle adaptation ...voltage-gated sodium channel activity involved in AV node cell action potential / voltage-gated sodium channel activity involved in bundle of His cell action potential / voltage-gated sodium channel activity involved in SA node cell action potential / bundle of His cell action potential / AV node cell action potential / sodium channel complex / SA node cell action potential / AV node cell to bundle of His cell communication / membrane depolarization during SA node cell action potential / response to denervation involved in regulation of muscle adaptation / cardiac ventricle development / regulation of ventricular cardiac muscle cell membrane depolarization / membrane depolarization during atrial cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane repolarization / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / regulation of sodium ion transmembrane transport / brainstem development / membrane depolarization during AV node cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during bundle of His cell action potential / positive regulation of action potential / atrial cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / telencephalon development / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / ventricular cardiac muscle cell action potential / sodium ion import across plasma membrane / cardiac muscle cell action potential involved in contraction / regulation of ventricular cardiac muscle cell membrane repolarization / sodium channel inhibitor activity / regulation of cardiac muscle cell contraction / voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / ankyrin binding / sodium ion transport / positive regulation of heart rate / nitric-oxide synthase binding / fibroblast growth factor binding / regulation of heart rate by cardiac conduction / odontogenesis of dentin-containing tooth / membrane depolarization / intercalated disc / sodium ion transmembrane transport / lateral plasma membrane / neuronal action potential / cardiac muscle contraction / T-tubule / cellular response to calcium ion / regulation of heart rate / bioluminescence / cerebellum development / generation of precursor metabolites and energy / caveola / positive regulation of epithelial cell proliferation / response to organic cyclic compound / sarcolemma / defense response / Z disc / toxin activity / scaffold protein binding / transmembrane transporter binding / calmodulin binding / symbiont entry into host cell / protein domain specific binding / axon / viral envelope / ubiquitin protein ligase binding / virion attachment to host cell / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / cell surface / endoplasmic reticulum / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
![]() | Jiang, D. / Catterall, W.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for Nav1.5 Opening Modulated by a Gating Modifier Toxin Authors: Jiang, D. / Catterall, W.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.8 KB | Display | ![]() |
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PDB format | ![]() | 171.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 46 KB | Display | |
Data in CIF | ![]() | 66.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33435MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 209037.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: rat cardiac sodium channel with a GFP-Flag tag fused at the C-terminus Source: (gene. exp.) ![]() ![]() ![]() Gene: Scn5a, G, GFP / Production host: ![]() |
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#2: Protein | Mass: 7065.984 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() References: UniProt: P56678 |
-Sugars , 2 types, 6 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/BMA.gif)
![](data/chem/img/BMA.gif)
#3: Sugar | ChemComp-NAG / #4: Sugar | ChemComp-BMA / | |
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-Non-polymers , 2 types, 7 molecules ![](data/chem/img/6OU.gif)
![](data/chem/img/9Z9.gif)
![](data/chem/img/9Z9.gif)
#5: Chemical | ChemComp-6OU / [( #6: Chemical | ChemComp-9Z9 / ( | |
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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 |
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Sample preparation
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Molecular weight | Value: 0.3 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||
Buffer solution | pH: 6.1 | ||||||||||||||||||||||||
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 198350 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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