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- PDB-6a90: Complex of voltage-gated sodium channel NavPaS from American cock... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a90 | ||||||||||||||||||||||||
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Title | Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana and Dc1a | ||||||||||||||||||||||||
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![]() | MEMBRANE PROTEIN/TOXIN / complex / sodium channel / toxin / MEMBRANE PROTEIN / MEMBRANE PROTEIN-TOXIN complex | ||||||||||||||||||||||||
Function / homology | ![]() host cell presynaptic membrane / membrane depolarization during action potential / voltage-gated sodium channel complex / voltage-gated sodium channel activity / neuronal action potential / sodium channel regulator activity / toxin activity / axon / extracellular region Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||||||||
![]() | 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. ...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. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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. | ||||||||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 261.5 KB | Display | ![]() |
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PDB format | ![]() | 203.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 62.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6995MC ![]() 6996C ![]() 6997C ![]() 6a91C ![]() 6a95C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 183875.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() | ||||
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#2: Protein | Mass: 6502.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Polysaccharide | #4: Sugar | #5: Chemical | ChemComp-NA / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 0.2 MDa / Experimental value: NO | ||||||||||||||||||||||||
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255265 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 2.8 Å | ||||||||||||||||||||||||
Refine LS restraints |
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