7DJI | pdb_00007dji

Crystal structure of Lymnaea stagnalis Acetylcholine binding protein (AChBP) complexed with Paraherquamide A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.184 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Determinants of subtype-selectivity of the anthelmintic paraherquamide A on Caenorhabditis elegans nicotinic acetylcholine receptors.

Koizumi, W.Otsubo, S.Furutani, S.Niki, K.Takayama, K.Fujimura, S.Maekawa, T.Koyari, R.Ihara, M.Kai, K.Hayashi, H.Ali, M.S.Kage-Nakadai, E.Sattelle, D.B.Matsuda, K.

(2023) Mol Pharmacol 

  • DOI: https://doi.org/10.1124/molpharm.122.000601
  • Primary Citation Related Structures: 
    7DJI

  • PubMed Abstract: 

    The anthelmintic paraherquamide A acts selectively on the nematode L-type nicotinic acetylcholine receptors (nAChRs), but the mechanism of its selectivity is unknown. This study targeted the basis of paraherquamide A selectivity by determining an X-ray crystal structure of the acetylcholine binding protein (AChBP), a surrogate nAChR ligand-binding domain, complexed with the compound and by measuring its actions on wild-type and mutant Caenorhabditis elegans nematodes and functionally expressed C. elegans nAChRs. Paraherquamide A showed a higher efficacy for the levamisole-sensitive [L-type (UNC-38/UNC-29/UNC-63/LEV-1/LEV-8)] nAChR than the nicotine-sensitive [N-type (ACR-16)] nAChR, a result consistent with in vivo studies on wild-type worms and worms with mutations in subunits of these two classes of receptors. The X-ray crystal structure of the Ls -AChBP-paraherquamide A complex and site-directed amino acid mutation studies showed for the first time that loop C, loop E, and loop F of the orthosteric receptor binding site play critical roles in the observed L-type nAChR selective actions of paraherquamide A. SIGNIFICANCE STATEMENT: Paraherquamide A, an oxindole alkaloid, has been shown to act selectively on the L-type over N-type nAChRs in nematodes, but the mechanism of selectivity is unknown. We have co-crystallized paraherquamide A with the acetylcholine binding protein, a surrogate of nAChRs, and found that structural features of loop C, loop E, and loop F contribute to the L-type nAChR selectivity of the alkaloid. The results create a new platform for the design of anthelmintic drugs targeting cholinergic neurotransmission in parasitic nematodes.


  • Organizational Affiliation
    • Department of Applied Biological Chemistry, Faculty of Agriculture (W.K., S.O., S.Fur., K.N., K.T., S.Fuj., T.M., R.K., M.I., K.M.) and Agricultural Technology and Innovation Research Institute (K.M.), Kindai University, Nara, Japan; Graduate School of Agriculture (K.K., H.H.) and Graduate School of Human Life and Ecology (M.S.A., E.K-N.), Osaka Metropolitan University, Osaka, Japan; Faculty of Food Science and Technology, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh (M.S.A.); and Centre for Respiratory Biology, UCL Respiratory, Division of Medicine, University College London, London, UK (D.B.S.).

Macromolecule Content 

  • Total Structure Weight: 124.68 kDa 
  • Atom Count: 8,936 
  • Modeled Residue Count: 1,026 
  • Deposited Residue Count: 1,070 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholine-binding protein
A, B, C, D, E
214Lymnaea stagnalisMutation(s): 0 
UniProt
Find proteins for P58154 (Lymnaea stagnalis)
Explore P58154 
Go to UniProtKB:  P58154
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58154
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H8U

Query on H8U



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D],
N [auth E]
Paraherquamide A
C28 H35 N3 O5
UVZZDDLIOJPDKX-ITKQZBBDSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.373α = 90
b = 74.373β = 90
c = 349.595γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan17H01472

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-24
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary