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- EMDB-9781: Structure of human voltage-gated sodium channel Nav1.7 in complex... -

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Entry
Database: EMDB / ID: 9781
TitleStructure of human voltage-gated sodium channel Nav1.7 in complex with auxiliary beta subunits, huwentoxin-IV and saxitoxin
Map data
SampleComplex of human voltage-gated sodium channel Nav1.7 with auxiliary beta subunits, huwentoxin-IV and saxitoxin
  • (Sodium channel subunit beta- ...) x 2
  • Sodium channel protein type 9 subunit alpha
  • (ligand) x 2
Function / homologySodium ion transport-associated / Voltage-dependent channel domain superfamily / IQ motif, EF-hand binding site / Myelin P0 protein-related / Voltage gated sodium channel, alpha subunit / Immunoglobulin subtype / Ion transport domain / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold ...Sodium ion transport-associated / Voltage-dependent channel domain superfamily / IQ motif, EF-hand binding site / Myelin P0 protein-related / Voltage gated sodium channel, alpha subunit / Immunoglobulin subtype / Ion transport domain / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Voltage-gated Na+ ion channel, cytoplasmic domain / Sodium channel subunit beta-1/beta-3 / Voltage gated sodium channel, alpha-9 subunit / Sodium channel subunit beta-2 / Immunoglobulin-like domain superfamily / Ion transport protein / Sodium ion transport-associated / Immunoglobulin V-set domain / Cytoplasmic domain of voltage-gated Na+ ion channel / Ig-like domain profile. / Interaction between L1 and Ankyrins / Phase 0 - rapid depolarisation / corticospinal neuron axon guidance / regulation of voltage-gated sodium channel activity / voltage-gated sodium channel activity involved in Purkinje myocyte action potential / response to pyrethroid / regulation of atrial cardiac muscle cell membrane depolarization / voltage-gated sodium channel activity involved in cardiac muscle cell action potential / membrane depolarization during Purkinje myocyte cell action potential / locomotion / cardiac conduction / regulation of sodium ion transmembrane transporter activity / membrane depolarization during cardiac muscle cell action potential / cardiac muscle cell action potential involved in contraction / voltage-gated sodium channel complex / membrane depolarization during action potential / regulation of ventricular cardiac muscle cell membrane repolarization / behavioral response to pain / node of Ranvier / neuronal action potential propagation / positive regulation of sodium ion transport / voltage-gated sodium channel activity / sodium channel inhibitor activity / sodium ion binding / neuronal action potential / sodium ion transmembrane transport / regulation of heart rate by cardiac conduction / sodium ion transport / voltage-gated ion channel activity / membrane depolarization / intercalated disc / regulation of ion transmembrane transport / T-tubule / cardiac muscle contraction / sodium channel regulator activity / sensory perception of pain / post-embryonic development / positive regulation of neuron projection development / response to toxic substance / nervous system development / axon guidance / chemical synaptic transmission / ion channel binding / cell adhesion / inflammatory response / axon / integral component of plasma membrane / extracellular region / plasma membrane / Sodium channel subunit beta-2 / Sodium channel subunit beta-1 / Sodium channel protein type 9 subunit alpha
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsShen H / Liu D / Lei J / Yan N
CitationJournal: Science / Year: 2019
Title: Structures of human Na1.7 channel in complex with auxiliary subunits and animal toxins.
Authors: Huaizong Shen / Dongliang Liu / Kun Wu / Jianlin Lei / Nieng Yan
Abstract: Voltage-gated sodium channel Na1.7 represents a promising target for pain relief. Here we report the cryo-electron microscopy structures of the human Na1.7-β1-β2 complex bound to two combinations ...Voltage-gated sodium channel Na1.7 represents a promising target for pain relief. Here we report the cryo-electron microscopy structures of the human Na1.7-β1-β2 complex bound to two combinations of pore blockers and gating modifier toxins (GMTs), tetrodotoxin with protoxin-II and saxitoxin with huwentoxin-IV, both determined at overall resolutions of 3.2 angstroms. The two structures are nearly identical except for minor shifts of voltage-sensing domain II (VSD), whose S3-S4 linker accommodates the two GMTs in a similar manner. One additional protoxin-II sits on top of the S3-S4 linker in VSD The structures may represent an inactivated state with all four VSDs "up" and the intracellular gate closed. The structures illuminate the path toward mechanistic understanding of the function and disease of Na1.7 and establish the foundation for structure-aided development of analgesics.
Validation ReportPDB-ID: 6j8g

SummaryFull report
PDB-ID: 6j8h

SummaryFull report
About validation report
DateDeposition: Jan 19, 2019 / Header (metadata) release: Feb 27, 2019 / Map release: Feb 27, 2019 / Last update: Feb 27, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6j8g
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6j8h
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9781.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.09 Å/pix.
= 261.84 Å
240 pix
1.09 Å/pix.
= 261.84 Å
240 pix
1.09 Å/pix.
= 261.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.24939026 - 0.41021213
Average (Standard dev.)0.0007113032 (0.011754235)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 261.84 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z261.840261.840261.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ364364364
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.2490.4100.001

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Supplemental data

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Sample components

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Entire Complex of human voltage-gated sodium channel Nav1.7 with auxilia...

EntireName: Complex of human voltage-gated sodium channel Nav1.7 with auxiliary beta subunits, huwentoxin-IV and saxitoxin
Number of components: 6

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Component #1: protein, Complex of human voltage-gated sodium channel Nav1.7 wit...

ProteinName: Complex of human voltage-gated sodium channel Nav1.7 with auxiliary beta subunits, huwentoxin-IV and saxitoxin
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-2

ProteinName: Sodium channel subunit beta-2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.355859 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Sodium channel protein type 9 subunit alpha

ProteinName: Sodium channel protein type 9 subunit alpha / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 231.211922 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Sodium channel subunit beta-1

ProteinName: Sodium channel subunit beta-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.732115 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #6: ligand, [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetr...

LigandName: [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.299286 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
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: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 275630
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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