2NAJ | pdb_00002naj

Solution structure of K2 lobe of double-knot toxin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2NAJ

This is version 1.2 of the entry. See complete history

Literature

Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin

Bae, C.Anselmi, C.Kalia, J.Jara-Oseguera, A.Schwieters, C.D.Krepkiy, D.Lee, C.W.Kim, E.H.Kim, J.I.Faraldo-Gomez, J.D.Swartz, K.J.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.11273
  • Primary Citation Related Structures: 
    2N9Z, 2NAJ

  • PubMed Abstract: 

    Venom toxins are invaluable tools for exploring the structure and mechanisms of ion channels. Here, we solve the structure of double-knot toxin (DkTx), a tarantula toxin that activates the heat-activated TRPV1 channel. We also provide improved structures of TRPV1 with and without the toxin bound, and investigate the interactions of DkTx with the channel and membranes. We find that DkTx binds to the outer edge of the external pore of TRPV1 in a counterclockwise configuration, using a limited protein-protein interface and inserting hydrophobic residues into the bilayer. We also show that DkTx partitions naturally into membranes, with the two lobes exhibiting opposing energetics for membrane partitioning and channel activation. Finally, we find that the toxin disrupts a cluster of hydrophobic residues behind the selectivity filter that are critical for channel activation. Collectively, our findings reveal a novel mode of toxin-channel recognition that has important implications for the mechanism of thermosensation.


  • Organizational Affiliation
    • Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.

Macromolecule Content 

  • Total Structure Weight: 3.69 kDa 
  • Atom Count: 253 
  • Modeled Residue Count: 33 
  • Deposited Residue Count: 33 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tau-theraphotoxin-Hs1a33Cyriopagopus schmidtiMutation(s): 0 
UniProt
Find proteins for P0CH43 (Cyriopagopus schmidti)
Explore P0CH43 
Go to UniProtKB:  P0CH43
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CH43
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary