7TXF | pdb_00007txf

The allosteric binding mode of alphaD-conotoxin VxXXB

• PDB DOI: https://doi.org/10.2210/pdb7TXF/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Lymnaea stagnalis, Conus vexillum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-09 Released: 2023-04-12 
• Deposition Author(s): Ho, T.N.T., Abraham, N., Lewis, R.J.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.246 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Unravelling the allosteric binding mode of alpha D-VxXXB at nicotinic acetylcholine receptors.

Ho, T.N., Abraham, N., Lewis, R.J.

(2023) Front Pharmacol 14: 1170514-1170514

• PubMed: 37124228 
• DOI: https://doi.org/10.3389/fphar.2023.1170514
• Primary Citation Related Structures: 
  7TXF


• PubMed Abstract: 
  

  αD-conotoxins are 11 kDa homodimers that potently inhibit nicotinic acetylcholine receptors (nAChRs) through a non-competitive (allosteric) mechanism. In this study, we describe the allosteric binding mode of the granulin-like C-terminal (CTD) of VxXXB bound to Lymnea stagnalis acetylcholine binding protein ( Ls -AChBP), a soluble homologue of the extracellular ligand-binding domain of nAChRs. This co-crystal complex revealed a novel allosteric binding site for nAChR antagonists outside the C-loop that caps the orthosteric site defined by the nAChR agonist nicotine and the antagonist epibatidine. Mutational and docking studies on Ls -AChBP supported a two-site binding mode for full-length VxXXB, with the first CTD binding site located outside the C-loop as seen in the co-crystal complex, with a second CTD binding site located near the N-terminal end of the adjacent subunit of AChBP. These results provide new structural insight into a novel allosteric mechanism of nAChR inhibition and define the cooperative binding mode of the N-terminal domain linked granulin core domains of αD-conotoxins.

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Organizational Affiliation: 
• Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A5B3 Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Local Symmetry: Cyclic - C5  (Explore in 3D)
Local Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 126.24 kDa 
• Atom Count: 8,771 
• Modeled Residue Count: 1,103 
• Deposited Residue Count: 1,115 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine-binding protein	A, B, C, D, E	205	Lymnaea stagnalis	Mutation(s): 0
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154  Go to UniProtKB:  P58154

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-conotoxin VxXXB	F, G, H	30	Conus vexillum	Mutation(s): 0
UniProt
Find proteins for P0C1W6 (Conus vexillum) Explore P0C1W6  Go to UniProtKB:  P0C1W6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.246 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.909	α = 90
b = 119.573	β = 90
c = 150.733	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Ho, T.N.T., Abraham, N., Lewis, R.J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	--

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2023-10-25
  Changes: Database references, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary