|Entry||Database: PDB / ID: 6agf|
|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||Immunoglobulin V-set domain / Sodium channel subunit beta-1/beta-3 / Voltage gated sodium channel, alpha subunit / Ion transport domain / Voltage gated sodium channel, alpha-4 subunit, mammalian / Sodium ion transport-associated / Immunoglobulin-like fold / Voltage-dependent channel domain superfamily / Immunoglobulin-like domain superfamily / Ion transport protein ...Immunoglobulin V-set domain / Sodium channel subunit beta-1/beta-3 / Voltage gated sodium channel, alpha subunit / Ion transport domain / Voltage gated sodium channel, alpha-4 subunit, mammalian / Sodium ion transport-associated / Immunoglobulin-like fold / Voltage-dependent channel domain superfamily / Immunoglobulin-like domain superfamily / Ion transport protein / Sodium ion transport-associated / Immunoglobulin V-set domain / IQ motif profile. / Interaction between L1 and Ankyrins / Phase 0 - rapid depolarisation / IQ motif, EF-hand binding site / corticospinal neuron axon guidance / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / response to pyrethroid / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of atrial cardiac muscle cell membrane depolarization / membrane depolarization during Purkinje myocyte cell action potential / cardiac conduction / locomotion / regulation of sodium ion transmembrane transporter activity / voltage-gated sodium channel complex / cardiac muscle cell action potential involved in contraction / membrane depolarization during cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell membrane repolarization / membrane depolarization during action potential / neuronal action potential propagation / node of Ranvier / positive regulation of sodium ion transport / voltage-gated sodium channel activity / sodium channel inhibitor activity / neuronal action potential / sodium ion transmembrane transport / regulation of heart rate by cardiac conduction / voltage-gated ion channel activity / sodium ion transport / membrane depolarization / intercalated disc / regulation of ion transmembrane transport / T-tubule / cardiac muscle contraction / sodium channel regulator activity / muscle contraction / positive regulation of neuron projection development / chemical synaptic transmission / axon guidance / cell adhesion / integral component of plasma membrane / extracellular region / plasma membrane / Sodium channel protein type 4 subunit alpha / Sodium channel subunit beta-1|
Function and homology information
|Specimen source||Homo sapiens (human)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution|
|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. / Xiong, W. / Gong, H.P. / Xiao, B.L. / Yan, N.|
|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.
SummaryFull reportAbout validation report
|Date||Deposition: Aug 11, 2018 / Release: Oct 10, 2018|
|Structure viewer||Molecule: |
Downloads & links
A: Sodium channel protein type 4 subunit alpha
B: Sodium channel subunit beta-1
-Sodium channel ... , 2 types, 2 molecules A
|#1: Protein/peptide|| |
Mass: 212643.562 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SCN4A / Production host: Homo sapiens (human) / References: UniProt: P35499
|#2: Protein/peptide|| |
Mass: 24706.920 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SCN1B / Production host: Homo sapiens (human) / References: UniProt: Q07699
-Non-polymers , 4 types, 16 molecules
|#4: Chemical|| ChemComp-BMA / ||#5: Chemical|
ChemComp-6OU / [(
|#6: Chemical|| ChemComp-9Z9 / (|
|Nonpolymer details||The complete structure of ligand 9Z9 is glyco-diosgenin. Only partial of the molecule was modeled.|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: single particle reconstruction|
|Molecular weight||Value: 0.2 MDa / Experimental value: NO|
|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
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope 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)|
|Software||Name: PHENIX / Version: 1.13_2998: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|3D reconstruction||Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 191936 / Symmetry type: POINT|
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