8XSU

Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein Q55R Mutant Complexed with Dinotefuran


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.196 

Starting Model: experimental
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Literature

Unravelling nicotinic receptor and ligand features underlying neonicotinoid knockdown actions on the malaria vector mosquito Anopheles gambiae.

Ito, R.Kamiya, M.Takayama, K.Mori, S.Matsumoto, R.Takebayashi, M.Ojima, H.Fujimura, S.Yamamoto, H.Ohno, M.Ihara, M.Okajima, T.Yamashita, A.Colman, F.Lycett, G.J.Sattelle, D.B.Matsuda, K.

(2024) Open Biol 14: 240057-240057

  • DOI: https://doi.org/10.1098/rsob.240057
  • Primary Citation of Related Structures:  
    8XSU

  • PubMed Abstract: 

    With the spread of resistance to long-established insecticides targeting Anopheles malaria vectors, understanding the actions of compounds newly identified for vector control is essential. With new commercial vector-control products containing neonicotinoids under development, we investigate the actions of 6 neonicotinoids (imidacloprid, thiacloprid, clothianidin, dinotefuran, nitenpyram and acetamiprid) on 13 Anopheles gambiae nicotinic acetylcholine receptor (nAChR) subtypes produced by expression of combinations of the Ag α 1, Ag α 2, Ag α 3, Ag α 8 and Ag β 1 subunits in Xenopus laevis oocytes, the Drosophila melanogaster orthologues of which we have previously shown to be important in neonicotinoid actions. The presence of the Ag α 2 subunit reduces neonicotinoid affinity for the mosquito nAChRs, whereas the Ag α 3 subunit increases it. Crystal structures of the acetylcholine binding protein (AChBP), an established surrogate for the ligand-binding domain, with dinotefuran bound, shows a unique target site interaction through hydrogen bond formation and CH-N interaction at the tetrahydrofuran ring. This is of interest as dinotefuran is also under trial as the toxic element in baited traps. Multiple regression analyses show a correlation between the efficacy of neonicotinoids for the Ag α 1/Ag α 2/Ag α 8/Ag β 1 nAChR, their hydrophobicity and their rate of knockdown of adult female An. gambiae , providing new insights into neonicotinoid features important for malaria vector control.


  • Organizational Affiliation

    Department of Applied Biological Chemistry, Faculty of Agriculture, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine-binding protein
A, B, C, E
210Lymnaea stagnalisMutation(s): 1 
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholine-binding protein206Lymnaea stagnalisMutation(s): 1 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
A1LW0 (Subject of Investigation/LOI)
Query on A1LW0

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D],
N [auth E]
2-methyl-1-nitro-3-[(tetrahydro-3-furanyl) methyl] guanidine
C7 H14 N4 O3
YKBZOVFACRVRJN-LURJTMIESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.196 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.149α = 90
b = 74.149β = 90
c = 350.306γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement

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)Japan22H02350
Japan Society for the Promotion of Science (JSPS)Japan16K21507

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-18
    Type: Initial release