|Entry||Database: PDB / ID: 6a90|
|Title||Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a|
|Keywords||MEMBRANE PROTEIN/TOXIN / complex / sodium channel / toxin / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TOXIN complex|
|Function / homology||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 ...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 source||Periplaneta americana (American cockroach)|
Diguetia canities (spider)
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 2.8 Å resolution|
|Authors||Shen, 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.|
|Citation||Journal: 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.
SummaryFull reportAbout validation report
|Date||Deposition: Jul 11, 2018 / Release: Aug 8, 2018|
|Structure viewer||Molecule: |
Downloads & links
A: Sodium channel protein PaFPC1
|#1: Protein/peptide|| |
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|| |
Mass: 6502.441 Da / Num. of mol.: 1 / Source: (gene. exp.) Diguetia canities (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P49126
|#4: Chemical|| ChemComp-NA / |
|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: 7.4|
|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: 1.11.1_2575: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 255265 / Algorithm: FOURIER SPACE / Symmetry type: POINT|
|Least-squares process||Highest resolution: 2.8 Å|
|Refine LS restraints|
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