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- EMDB-6995: Complex of voltage-gated sodium channel NavPaS from American cock... -

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Basic information

Entry
Database: EMDB / ID: 6995
TitleComplex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a
Map data
Samplecomplex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a
  • voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana
  • Dc1a
  • Sodium channel protein PaFPC1
  • Mu-diguetoxin-Dc1a
  • (ligand) x 2
Function / homologyIon transport domain / Voltage-dependent channel domain superfamily / Spider Toxins mu-diguetoxin-1 a, b and c / Voltage-dependent L-type calcium channel, IQ-associated / Ion transport protein / Mu-diguetoxin-1 / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage gated sodium channel, alpha subunit / voltage-gated sodium channel complex / voltage-gated sodium channel activity ...Ion transport domain / Voltage-dependent channel domain superfamily / Spider Toxins mu-diguetoxin-1 a, b and c / Voltage-dependent L-type calcium channel, IQ-associated / Ion transport protein / Mu-diguetoxin-1 / Voltage-dependent L-type calcium channel, IQ-associated domain / Voltage gated sodium channel, alpha subunit / voltage-gated sodium channel complex / voltage-gated sodium channel activity / voltage-gated ion channel activity / other organism presynaptic membrane / regulation of ion transmembrane transport / toxin activity / extracellular region / Sodium channel protein PaFPC1 / Mu-diguetoxin-Dc1a
Function and homology information
SourcePeriplaneta americana (American cockroach) / Diguetia canities (spider)
Methodsingle particle reconstruction / cryo EM / 2.8 Å resolution
AuthorsShen HZ / li ZQ / Jiang Y / Pan XJ / Wu JP / Cristofori-Armstrong B / Smith JJ / Chin YKY / Lei JL / Zhou Q / King GF / Yan N
CitationJournal: Science / Year: 2018
Title: Structural basis for the modulation of voltage-gated sodium channels by animal toxins.
Authors: Huaizong Shen / Zhangqiang Li / Yan Jiang / Xiaojing Pan / Jianping Wu / Ben Cristofori-Armstrong / Jennifer J Smith / Yanni K Y Chin / Jianlin Lei / Qiang Zhou / Glenn F King / Nieng Yan
Abstract: Animal toxins that modulate the activity of Na channels are broadly divided into two categories-pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and saxitoxin (STX) are ...Animal toxins that modulate the activity of Na channels are broadly divided into two categories-pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and saxitoxin (STX) are responsible for pufferfish and shellfish poisoning in humans, respectively. Here we present structures of the insect Na channel NaPaS bound to a gating modifier toxin Dc1a at 2.8 Å and in the presence of TTX or STX at 2.6 Å and 3.2 Å resolution, respectively. Dc1a inserts into the cleft between VSD and the pore of NaPaS, making key contacts with both domains. The structures with bound TTX or STX reveal the molecular details for the specific blockade of Na access to the selectivity filter from the extracellular side by these guanidinium toxins. The structures shed light on structure-based development of Na channel drugs.
Validation ReportPDB-ID: 6a90

SummaryFull reportAbout validation report
DateDeposition: Jul 11, 2018 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Aug 8, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6a90
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6995.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.09 Å/pix.
= 349.12 Å
320 pix
1.09 Å/pix.
= 349.12 Å
320 pix
1.09 Å/pix.
= 349.12 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:0.08 (by author), 0.08 (movie #1):
Minimum - Maximum-0.22111739 - 0.36182782
Average (Standard dev.)0.00005174776 (0.008009242)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.0.0.
Limit319.319.319.
Spacing320320320
CellA=B=C: 349.12 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/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2210.3620.000

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Supplemental data

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Sample components

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Entire complex of voltage-gated sodium channel NavPaS from American cock...

EntireName: complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a
Number of components: 7

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Component #1: protein, complex of voltage-gated sodium channel NavPaS from Amer...

ProteinName: complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a
Recombinant expression: No
MassTheoretical: 200 kDa

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Component #2: protein, voltage-gated sodium channel NavPaS from American cockro...

ProteinName: voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana
Recombinant expression: No
SourceSpecies: Periplaneta americana (American cockroach)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Dc1a

ProteinName: Dc1a / Recombinant expression: No
SourceSpecies: Diguetia canities (spider)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Sodium channel protein PaFPC1

ProteinName: Sodium channel protein PaFPC1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 183.875422 kDa
SourceSpecies: Periplaneta americana (American cockroach)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Mu-diguetoxin-Dc1a

ProteinName: Mu-diguetoxin-Dc1a / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.502441 kDa
SourceSpecies: Diguetia canities (spider)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 7 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #7: ligand, SODIUM ION

LigandName: SODIUM IONSodium / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.29905 MDa

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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 / Applied symmetry: C1 (asymmetric) / Number of projections: 255265
3D reconstructionAlgorithm: FOURIER SPACE / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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