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- EMDB-30851: Voltage-gated sodium channel Nav1.1 and beta4 -

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Basic information

Entry
Database: EMDB / ID: EMD-30851
TitleVoltage-gated sodium channel Nav1.1 and beta4
Map data
SampleVoltage-gated sodium channelSodium channel:
(Sodium channel ...) x 2 / (ligand) x 2
Function / homology
Function and homology information


AV node cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / cardiac muscle cell action potential involved in contraction / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / voltage-gated sodium channel complex / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of sodium ion transport / voltage-gated sodium channel activity ...AV node cell action potential / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / regulation of sodium ion transmembrane transporter activity / cardiac muscle cell action potential involved in contraction / membrane depolarization during cardiac muscle cell action potential / membrane depolarization during action potential / voltage-gated sodium channel complex / regulation of ventricular cardiac muscle cell membrane repolarization / positive regulation of sodium ion transport / voltage-gated sodium channel activity / neuronal action potential / sodium ion transport / regulation of heart rate by cardiac conduction / voltage-gated ion channel activity / intrinsic component of plasma membrane / sodium ion transmembrane transport / intercalated disc / cardiac muscle contraction / sodium channel regulator activity / regulation of ion transmembrane transport / cation channel activity / detection of mechanical stimulus involved in sensory perception of pain / Z disc / ion channel binding / nuclear body / axon / nucleoplasm / plasma membrane
Voltage gated sodium channel, alpha-1 subunit / Voltage-gated cation channel calcium and sodium / Immunoglobulin-like domain superfamily / Voltage-dependent channel domain superfamily / Voltage-gated Na+ ion channel, cytoplasmic domain / Immunoglobulin-like fold / Immunoglobulin V-set domain / Sodium ion transport-associated / Immunoglobulin-like domain / Ion transport domain ...Voltage gated sodium channel, alpha-1 subunit / Voltage-gated cation channel calcium and sodium / Immunoglobulin-like domain superfamily / Voltage-dependent channel domain superfamily / Voltage-gated Na+ ion channel, cytoplasmic domain / Immunoglobulin-like fold / Immunoglobulin V-set domain / Sodium ion transport-associated / Immunoglobulin-like domain / Ion transport domain / Immunoglobulin subtype / Voltage gated sodium channel, alpha subunit / Myelin P0 protein-related
Sodium channel protein type 1 subunit alpha / Sodium channel subunit beta-4
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYan N / Pan X / Li Z / Huang G
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0500402 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Comparative structural analysis of human Na1.1 and Na1.5 reveals mutational hotspots for sodium channelopathies.
Authors: Xiaojing Pan / Zhangqiang Li / Xueqin Jin / Yanyu Zhao / Gaoxingyu Huang / Xiaoshuang Huang / Zilin Shen / Yong Cao / Mengqiu Dong / Jianlin Lei / Nieng Yan /
Abstract: Among the nine subtypes of human voltage-gated sodium (Na) channels, the brain and cardiac isoforms, Na1.1 and Na1.5, each carry more than 400 missense mutations respectively associated with epilepsy ...Among the nine subtypes of human voltage-gated sodium (Na) channels, the brain and cardiac isoforms, Na1.1 and Na1.5, each carry more than 400 missense mutations respectively associated with epilepsy and cardiac disorders. High-resolution structures are required for structure-function relationship dissection of the disease variants. We report the cryo-EM structures of the full-length human Na1.1-β4 complex at 3.3 Å resolution here and the Na1.5-E1784K variant in the accompanying paper. Up to 341 and 261 disease-related missense mutations in Na1.1 and Na1.5, respectively, are resolved. Comparative structural analysis reveals several clusters of disease mutations that are common to both Na1.1 and Na1.5. Among these, the majority of mutations on the extracellular loops above the pore domain and the supporting segments for the selectivity filter may impair structural integrity, while those on the pore domain and the voltage-sensing domains mostly interfere with electromechanical coupling and fast inactivation. Our systematic structural delineation of these mutations provides important insight into their pathogenic mechanism, which will facilitate the development of precise therapeutic interventions against various sodium channelopathies.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJan 4, 2021-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dtd
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30851.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 219.58 Å
1.1 Å/pix.
x 200 pix.
= 219.58 Å
1.1 Å/pix.
x 200 pix.
= 219.58 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.02
Minimum - Maximum-0.08521426 - 0.16246283
Average (Standard dev.)0.0005779475 (±0.005417547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 219.58 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09791.09791.0979
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z219.580219.580219.580
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0850.1620.001

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Supplemental data

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Sample components

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Entire Voltage-gated sodium channel

EntireName: Voltage-gated sodium channelSodium channel / Number of components: 5

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Component #1: protein, Voltage-gated sodium channel

ProteinName: Voltage-gated sodium channelSodium channel / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Sodium channel subunit beta-4

ProteinName: Sodium channel subunit beta-4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.00098 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Sodium channel protein type 1 subunit alpha

ProteinName: Sodium channel protein type 1 subunit alpha / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 233.796141 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)b...

LigandName: (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.544805 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 133127
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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