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: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 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: https://doi.org/10.1126/science.aau2596
  • Primary Citation of Related Structures:  
    6A90, 6A91, 6A95

  • PubMed Abstract: 

    • 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 ...

    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: 

    Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium channel protein PaFPC11,596Periplaneta americanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0E0C2 (Periplaneta americana)
Explore D0E0C2 
Go to UniProtKB:  D0E0C2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0E0C2
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mu-diguetoxin-Dc1a57Diguetia canitiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P49126 (Diguetia canities)
Explore P49126 
Go to UniProtKB:  P49126
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49126
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9SR
Query on 9SR
Download Ideal Coordinates CCD File 
H [auth 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)
C11 H17 N3 O8
CFMYXEVWODSLAX-QOZOJKKESA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

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View more in-depth experimental data
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  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary