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Yorodumi- PDB-6agf: Structure of the human voltage-gated sodium channel Nav1.4 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6agf | |||||||||||||||||||||
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Title | Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta1 | |||||||||||||||||||||
Components | (Sodium channel ...) x 2 | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / sodium channel | |||||||||||||||||||||
Function / homology | Function and homology information regulation of skeletal muscle contraction by action potential / corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / membrane depolarization during Purkinje myocyte cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / voltage-gated sodium channel complex ...regulation of skeletal muscle contraction by action potential / corticospinal neuron axon guidance / positive regulation of voltage-gated sodium channel activity / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / membrane depolarization during Purkinje myocyte cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / cardiac conduction / voltage-gated sodium channel complex / membrane depolarization during cardiac muscle cell action potential / positive regulation of sodium ion transport / node of Ranvier / cardiac muscle cell action potential involved in contraction / high voltage-gated calcium channel activity / locomotion / voltage-gated sodium channel activity / regulation of ventricular cardiac muscle cell membrane repolarization / sodium channel inhibitor activity / neuronal action potential propagation / Interaction between L1 and Ankyrins / sodium ion transport / voltage-gated calcium channel complex / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / membrane depolarization / calcium ion import across plasma membrane / intercalated disc / sodium channel regulator activity / sodium ion transmembrane transport / cardiac muscle contraction / T-tubule / muscle contraction / axon guidance / Sensory perception of sweet, bitter, and umami (glutamate) taste / positive regulation of neuron projection development / perikaryon / transmembrane transporter binding / cell adhesion / extracellular region / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||||||||||||||
Authors | Pan, X.J. / li, Z.Q. / Zhou, Q. / Shen, H.Z. / Wu, K. / Huang, X.S. / Chen, J.F. / Zhang, J.R. / Zhu, X.C. / Lei, J.L. ...Pan, X.J. / li, Z.Q. / Zhou, Q. / Shen, H.Z. / Wu, K. / Huang, X.S. / Chen, J.F. / Zhang, J.R. / Zhu, X.C. / Lei, J.L. / Xiong, W. / Gong, H.P. / Xiao, B.L. / Yan, N. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: Science / Year: 2018 Title: Structure of the human voltage-gated sodium channel Na1.4 in complex with β1. Authors: Xiaojing Pan / Zhangqiang Li / Qiang Zhou / Huaizong Shen / Kun Wu / Xiaoshuang Huang / Jiaofeng Chen / Juanrong Zhang / Xuechen Zhu / Jianlin Lei / Wei Xiong / Haipeng Gong / Bailong Xiao / Nieng Yan / Abstract: Voltage-gated sodium (Na) channels, which are responsible for action potential generation, are implicated in many human diseases. Despite decades of rigorous characterization, the lack of a structure ...Voltage-gated sodium (Na) channels, which are responsible for action potential generation, are implicated in many human diseases. Despite decades of rigorous characterization, the lack of a structure of any human Na channel has hampered mechanistic understanding. Here, we report the cryo-electron microscopy structure of the human Na1.4-β1 complex at 3.2-Å resolution. Accurate model building was made for the pore domain, the voltage-sensing domains, and the β1 subunit, providing insight into the molecular basis for Na permeation and kinetic asymmetry of the four repeats. Structural analysis of reported functional residues and disease mutations corroborates an allosteric blocking mechanism for fast inactivation of Na channels. The structure provides a path toward mechanistic investigation of Na channels and drug discovery for Na channelopathies. | |||||||||||||||||||||
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 | 6agf.cif.gz | 268.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6agf.ent.gz | 206.9 KB | Display | PDB format |
PDBx/mmJSON format | 6agf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6agf ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6agf | HTTPS FTP |
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-Related structure data
Related structure data | 9617MC 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
-Sodium channel ... , 2 types, 2 molecules AB
#1: Protein | Mass: 212836.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4A / Production host: Homo sapiens (human) / References: UniProt: P35499 |
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#2: Protein | Mass: 24732.115 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SCN1B / Production host: Homo sapiens (human) / References: UniProt: Q07699 |
-Sugars , 3 types, 5 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ||
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#4: Polysaccharide | #7: Sugar | |
-Non-polymers , 2 types, 7 molecules
#5: Chemical | ChemComp-6OU / [( #6: Chemical | ChemComp-9Z9 / ( | |
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-Details
Nonpolymer details | The complete structure of ligand 9Z9 is glyco-diosgenin. Only partial of the molecule was modeled. |
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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 |
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Molecular weight | Value: 0.2 MDa / Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 5.9 | ||||||||||||||||||||||||
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 |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191936 / Symmetry type: POINT |