6N4R

CryoEM structure of Nav1.7 VSD2 (deactived state) in complex with the gating modifier toxin ProTx2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Nav1.7 Inhibition by a Gating-Modifier Spider Toxin.

Xu, H.Li, T.Rohou, A.Arthur, C.P.Tzakoniati, F.Wong, E.Estevez, A.Kugel, C.Franke, Y.Chen, J.Ciferri, C.Hackos, D.H.Koth, C.M.Payandeh, J.

(2019) Cell 176: 702

  • DOI: 10.1016/j.cell.2018.12.018
  • Primary Citation of Related Structures:  
    6N4Q, 6N4R, 6N4I

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Structural Biology, Genentech, South San Francisco, CA 94080, USA. Electronic address: payandeh.jian@gene.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nav1.7 VSD2-NavAb chimeraL [auth A], A [auth B], B [auth C], C [auth D]288Aliarcobacter butzleri RM4018Homo sapiensMutation(s): 0 
Gene Names: Abu_1752SCN9ANENA
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for A8EVM5 (Arcobacter butzleri (strain RM4018))
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Go to UniProtKB:  A8EVM5
Find proteins for Q15858 (Homo sapiens)
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Go to UniProtKB:  Q15858
PHAROS:  Q15858
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta/omega-theraphotoxin-Tp2aD [auth E], E [auth F], F [auth G], G [auth H]30Thrixopelma pruriensMutation(s): 0 
UniProt
Find proteins for P83476 (Thrixopelma pruriens)
Explore P83476 
Go to UniProtKB:  P83476
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chainH [auth I], J [auth K]215Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fab heavy chainI [auth J], K [auth L]228Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Other