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- PDB-9she: Structure of the honeybee GABAA RDL receptor with GABA and Abamectin -

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Basic information

Entry
Database: PDB / ID: 9she
TitleStructure of the honeybee GABAA RDL receptor with GABA and Abamectin
ComponentsGamma-aminobutyric acid receptor subunit beta
KeywordsMEMBRANE PROTEIN / GABAA receptor / insect / neurotransmission / insecticides
Function / homology
Function and homology information


ligand-gated monoatomic anion channel activity / GABA-A receptor activity / chloride channel activity / chloride channel complex / extracellular ligand-gated monoatomic ion channel activity / postsynaptic membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain ...Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
: / GAMMA-AMINO-BUTANOIC ACID / Gamma-aminobutyric acid receptor subunit beta
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLaboure, T. / Nury, H.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Neuron / Year: 2026
Title: Structures of the honeybee GABA RDL receptor illuminate allosteric modulation.
Authors: Tatiana Labouré / Mayank Prakash Pandey / Eleftherios Zarkadas / Céline Juillan-Binard / Delphine Baud / Jacques Neyton / Thierry Cens / Matthieu Rousset / François Dehez / Pierre Charnet / Hugues Nury /
Abstract: A large share of insecticides targets insect ion channels. In particular, the GABA RDL (resistant to dieldrin) receptor is targeted by old pore blockers or more recent allosteric modulators binding ...A large share of insecticides targets insect ion channels. In particular, the GABA RDL (resistant to dieldrin) receptor is targeted by old pore blockers or more recent allosteric modulators binding to a cavity of its transmembrane domain. Here, we describe three ligand-binding sites and the associated receptor conformations, using a combination of cryoelectron microscopy (cryo-EM), electrophysiology, and molecular dynamics. The GABA site geometry is well conserved with that of mammalian receptors, in line with the absence of orthosteric insecticide. The transmembrane modulation site, occupied here by abamectin, exists in a closed-pore conformation. We identify a second allosteric transmembrane site using a compound named chrodrimanin B. Structures also reveal the existence of a conformation-dependent PIP lipid site. We anticipate our results to be the starting point for investigations on the physiological modulation of insect GABA receptors. The honeybee receptor structures may also foster the search for species-specific, environmentally benign insecticides.
History
DepositionAug 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor subunit beta
C: Gamma-aminobutyric acid receptor subunit beta
B: Gamma-aminobutyric acid receptor subunit beta
D: Gamma-aminobutyric acid receptor subunit beta
E: Gamma-aminobutyric acid receptor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,68025
Polymers267,5875
Non-polymers7,09320
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Gamma-aminobutyric acid receptor subunit beta


Mass: 53517.445 Da / Num. of mol.: 5 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Apis mellifera (honey bee) / Gene: RDL, 406124, LOC406124
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: A0A8U0Y4W2
#2: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, inhibitor*YM
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-A1JNZ / Abamectin / (1'R,2R,3S,4'S,6S,8'R,10'E,10'R,12'S,13'S,21'R,24'S)-2-[(2S)-butan-2-yl]-12'-[(2R,4S,5S,6S)-4-methoxy-5-[(2S,4S,5S,6S)-4-methoxy-6-methyl-5-oxidanyl-oxan-2-yl]oxy-6-methyl-oxan-2-yl]oxy-3,11',13',22'-tetramethyl-21',24'-bis(oxidanyl)spiro[2,3-dihydropyran-6,6'-3,7,19-trioxatetracyclo[15.6.1.1^{4,8}.1^{20,24}]pentacosa-10,14,16,22-tetraene]-2'-one


Mass: 873.077 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C48H72O14 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Gamma-aminobutyric acid receptor subunit beta, RDL in complex with GABA and Abamectin
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Apis mellifera (honey bee)
Source (recombinant)Organism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 59.86 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2PHENIXdev_5480model refinement
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30111 / Symmetry type: POINT

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