[English] 日本語
EMN Papers
- Database of articles cited by 3DEM data entries -

+
Search query

Keywords
Author
Journal
IF

-
Structure paper

TitleStructural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin.
Journal, issue, pagesCell, Vol. 176, Issue 4, Page 702-715.e14, Year 2019
Publish dateFeb 7, 2019
AuthorsHui Xu / Tianbo Li / Alexis Rohou / Christopher P Arthur / Foteini Tzakoniati / Evera Wong / Alberto Estevez / Christine Kugel / Yvonne Franke / Jun Chen / Claudio Ciferri / David H Hackos / Christopher M Koth / Jian Payandeh /
PubMed AbstractVoltage-gated sodium (Nav) channels are targets of disease mutations, toxins, and therapeutic drugs. Despite recent advances, the structural basis of voltage sensing, electromechanical coupling, and ...Voltage-gated sodium (Nav) channels are targets of disease mutations, toxins, and therapeutic drugs. Despite recent advances, the structural basis of voltage sensing, electromechanical coupling, and toxin modulation remains ill-defined. Protoxin-II (ProTx2) from the Peruvian green velvet tarantula is an inhibitor cystine-knot peptide and selective antagonist of the human Nav1.7 channel. Here, we visualize ProTx2 in complex with voltage-sensor domain II (VSD2) from Nav1.7 using X-ray crystallography and cryoelectron microscopy. Membrane partitioning orients ProTx2 for unfettered access to VSD2, where ProTx2 interrogates distinct features of the Nav1.7 receptor site. ProTx2 positions two basic residues into the extracellular vestibule to antagonize S4 gating-charge movement through an electrostatic mechanism. ProTx2 has trapped activated and deactivated states of VSD2, revealing a remarkable ∼10 Å translation of the S4 helix, providing a structural framework for activation gating in voltage-gated ion channels. Finally, our results deliver key templates to design selective Nav channel antagonists.
External linksCell / PubMed:30661758
MethodsEM (single particle) / X-ray diffraction
Resolution3.541 - 4.2 Å
Structure data

0341

6n4q

EMDB-0341, PDB-6n4q:
CryoEM structure of Nav1.7 VSD2 (actived state) in complex with the gating modifier toxin ProTx2
Method: EM (single particle) / Resolution: 3.6 Å

0342

6n4r

EMDB-0342, PDB-6n4r:
CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2
Method: EM (single particle) / Resolution: 4.2 Å

PDB-6n4i:
Structural basis of Nav1.7 inhibition by a gating-modifier spider toxin
Method: X-RAY DIFFRACTION / Resolution: 3.541 Å

Chemicals

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

Source
  • homo sapiens (human)
  • arcobacter butzleri (strain rm4018) (bacteria)
  • thrixopelma pruriens (green velvet)
  • mouse (mice)
  • mus musculus (house mouse)
KeywordsMETAL TRANSPORT / sodium channel / toxin / gating-modifier / voltage-gated / MEMBRANE PROTEIN / voltage-gated sodium channel / gating modifier toxin

+
About EMN Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Oct 5, 2021. Nobel Prize for mechanically activated and temperature-gated ion channels

Nobel Prize for mechanically activated and temperature-gated ion channels

  • The Nobel Prize in Physiology or Medicine 2021 was awarded jointly to David Julius and Ardem Patapoutian "for their discoveries of receptors for temperature and touch."
  • EM Navigator can help to find cryo-EM structure data by both pioneers.

External links:The Nobel Prize in Physiology or Medicine 2021 - NobelPrize.org / Structure data by Ardem Patapoutian / Structure data by David Julius

+
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jul 5, 2019. Downlodablable text data

Downlodablable text data

Some data of EM Navigator services can be downloaded as text file. Software such as Excel can load the data files.

PageDataFormat
EMN Searchsearch resultCSV, TSV, or JSON
EMN statisticsdata tableCSV or TSV

Related info.:EMN Search / EMN Statistics

-
EMN Papers

Database of articles cited by 3DEM data entries

  • Database of articles cited by 3DEM data entries in EMDB and PDB
  • Using PubMed data

Related info.:EMDB / PDB / Q: What are the data sources of EM Navigator? / EM Navigator / Yorodumi Papers / Changes in new EM Navigator and Yorodumi

Read more