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- PDB-6a90: Complex of voltage-gated sodium channel NavPaS from American cock... -

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Basic information

Entry
Database: PDB / ID: 6a90
TitleComplex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a
Components
  • Mu-diguetoxin-Dc1a
  • Sodium channel protein PaFPC1
KeywordsMEMBRANE PROTEIN/TOXIN / complex / sodium channel / toxin / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TOXIN complex
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
Specimen sourcePeriplaneta americana (American cockroach)
Diguetia canities (spider)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.8 Å resolution
AuthorsShen, H.Z. / li, Z.Q. / Jiang, Y. / Pan, X.J. / Wu, J.P. / Cristofori-Armstrong, B. / Smith, J.J. / Chin, Y.K.Y. / Lei, J.L. / Zhou, Q. / King, G.F. / 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 voltage-gated sodium (Na) channels are broadly divided into two categories-pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and ...Animal toxins that modulate the activity of voltage-gated sodium (Na) channels are broadly divided into two categories-pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and saxitoxin (STX) are responsible for puffer fish 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 angstrom-resolution 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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 11, 2018 / Release: Aug 8, 2018

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Structure visualization

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Assembly

Deposited unit
A: Sodium channel protein PaFPC1
B: Mu-diguetoxin-Dc1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,94910
Polyers190,3782
Non-polymers1,5718
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)4160
ΔGint (kcal/M)1
Surface area (Å2)71710

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Components

#1: Protein/peptide Sodium channel protein PaFPC1 / / Voltage-gated sodium channel / PaFPC1 / NavPaS


Mass: 183875.422 Da / Num. of mol.: 1
Source: (gene. exp.) Periplaneta americana (American cockroach)
Production host: Homo sapiens (human) / References: UniProt: D0E0C2
#2: Protein/peptide Mu-diguetoxin-Dc1a / Mu-DGTX-Dc1a / Insecticidal toxin DTX9.2


Mass: 6502.441 Da / Num. of mol.: 1 / Source: (gene. exp.) Diguetia canities (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P49126
#3: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 7 / Formula: C8H15NO6 / N-Acetylglucosamine
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1aCOMPLEX1, 20RECOMBINANT
2voltage-gated sodium channel NavPaS from American cockroach Periplaneta americanaCOMPLEX11RECOMBINANT
3Dc1aCOMPLEX21RECOMBINANT
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
126978Periplaneta americana (American cockroach)
2338407Diguetia canities (spider)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens (human)
23562Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 255265 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Least-squares processHighest resolution: 2.8 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01111389
ELECTRON MICROSCOPYf_angle_d1.25915499
ELECTRON MICROSCOPYf_dihedral_angle_d11.6796582
ELECTRON MICROSCOPYf_chiral_restr0.0711775
ELECTRON MICROSCOPYf_plane_restr0.0071913

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