6A95

Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta americana bound with tetrodotoxin and Dc1a


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the modulation of voltage-gated sodium channels by animal toxins.

Shen, H.Li, Z.Jiang, Y.Pan, X.Wu, J.Cristofori-Armstrong, B.Smith, J.J.Chin, Y.K.Y.Lei, J.Zhou, Q.King, G.F.Yan, N.

(2018) Science 362: --

  • DOI: 10.1126/science.aau2596
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Animal toxins that modulate the activity of voltage-gated sodium (Na <sub>v </sub>) channels are broadly divided into two categories-pore blockers and gating modifiers. The pore blockers tetrodotoxin (TTX) and saxitoxin (STX) are responsible for puff ...

    Animal toxins that modulate the activity of voltage-gated sodium (Na v ) 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 v channel Na v PaS 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 II and the pore of Na v PaS, 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 v channel drugs.


    Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia. nyan@princeton.edu glenn.king@imb.uq.edu.au zhouq2015@mail.tsinghua.edu.cn.,Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,State Key Laboratory of Membrane Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China. nyan@princeton.edu glenn.king@imb.uq.edu.au zhouq2015@mail.tsinghua.edu.cn.,Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium channel protein PaFPC1
A
1596Periplaneta americanaMutation(s): 0 
Find proteins for D0E0C2 (Periplaneta americana)
Go to UniProtKB:  D0E0C2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mu-diguetoxin-Dc1a
B
57Diguetia canitiesMutation(s): 0 
Find proteins for P49126 (Diguetia canities)
Go to UniProtKB:  P49126
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
9SR
Query on 9SR

Download SDF File 
Download CCD File 
A
(1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.1~7,11~.0~1,6~]tetradec-3-ene-5,9,12,13,14-pentol (non-preferred name)
Tetrodotoxin
C11 H17 N3 O8
CFMYXEVWODSLAX-QOZOJKKESA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2015CB910101
Ministry of Science and Technology (China)China2016YFA0500402
National Natural Science Foundation of ChinaChina31621092
National Natural Science Foundation of ChinaChina31630017
National Natural Science Foundation of ChinaChina31611130036
Australian Research CouncilAustraliaDP160104411
National Health and Medical Research Council (Australia)AustraliaAPP1072113

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references
  • Version 1.2: 2019-11-06
    Type: Data collection, Other