4X9Z | pdb_00004x9z

Dimeric conotoxin alphaD-GeXXA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Conotoxin alpha D-GeXXA utilizes a novel strategy to antagonize nicotinic acetylcholine receptors

Xu, S.Zhang, T.Kompella, S.N.Yan, M.Lu, A.Wang, Y.Shao, X.Chi, C.Adams, D.J.Ding, J.Wang, C.

(2015) Sci Rep 5: 14261-14261

  • DOI: https://doi.org/10.1038/srep14261
  • Primary Citation Related Structures: 
    4X9Z

  • PubMed Abstract: 

    Nicotinic acetylcholine receptors (nAChRs) play essential roles in transmitting acetylcholine-mediated neural signals across synapses and neuromuscular junctions, and are also closely linked to various diseases and clinical conditions. Therefore, novel nAChR-specific compounds have great potential for both neuroscience research and clinical applications. Conotoxins, the peptide neurotoxins produced by cone snails, are a rich reservoir of novel ligands that target receptors, ion channels and transporters in the nervous system. From the venom of Conus generalis, we identified a novel dimeric nAChR-inhibiting αD-conotoxin GeXXA. By solving the crystal structure and performing structure-guided dissection of this toxin, we demonstrated that the monomeric C-terminal domain of αD-GeXXA, GeXXA-CTD, retains inhibitory activity against the α9α10 nAChR subtype. Furthermore, we identified that His7 of the rat α10 nAChR subunit determines the species preference of αD-GeXXA, and is probably part of the binding site of this toxin. These results together suggest that αD-GeXXA cooperatively binds to two inter-subunit interfaces on the top surface of nAChR, thus allosterically disturbing the opening of the receptor. The novel antagonistic mechanism of αD-GeXXA via a new binding site on nAChRs provides a valuable basis for the rational design of new nAChR-targeting compounds.


  • Organizational Affiliation
    • Institute of Protein Research, Tongji University, 1239 Siping Road, Shanghai 200092, China.

Macromolecule Content 

  • Total Structure Weight: 11.29 kDa 
  • Atom Count: 794 
  • Modeled Residue Count: 95 
  • Deposited Residue Count: 100 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
alphaD-conotoxin GeXXA from the venom of Conus generalis
A, B
50Conus generalisMutation(s): 0 
UniProt
Find proteins for A0A0A0VBX4 (Conus generalis)
Explore A0A0A0VBX4 
Go to UniProtKB:  A0A0A0VBX4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A0VBX4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.436α = 90
b = 42.423β = 90
c = 83.013γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
ACORNphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-02
    Type: Initial release
  • Version 1.1: 2020-02-05
    Changes: Data collection, Derived calculations
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Structure summary