[English] 日本語
Yorodumi
- EMDB-54897: Structure of the honeybee GABAA RDL receptor with GABA and Abamectin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-54897
TitleStructure of the honeybee GABAA RDL receptor with GABA and Abamectin
Map data
Sample
  • Complex: Gamma-aminobutyric acid receptor subunit beta, RDL in complex with GABA and Abamectin
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: Abamectin
KeywordsGABAA receptor / insect / neurotransmission / insecticides / MEMBRANE PROTEIN
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-aminobutyric acid receptor subunit beta
Similarity search - Component
Biological speciesApis mellifera (honey bee)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLaboure T / Nury H
Funding support France, 1 items
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, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_54897.png

Downloads & links

-
Map

FileDownload / File: emd_54897.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å		0.94 Å/pix.
x 320 pix.
= 300.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.89
Minimum - Maximum-0.12090932 - 17.235890999999999
Average (Standard dev.)-0.031117892 (±0.48482424)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 300.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_54897_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #2

Fileemd_54897_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_54897_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_54897_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_54897_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Gamma-aminobutyric acid receptor subunit beta, RDL in complex wit...

EntireName: Gamma-aminobutyric acid receptor subunit beta, RDL in complex with GABA and Abamectin
Components
  • Complex: Gamma-aminobutyric acid receptor subunit beta, RDL in complex with GABA and Abamectin
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: Abamectin

-
Supramolecule #1: Gamma-aminobutyric acid receptor subunit beta, RDL in complex wit...

SupramoleculeName: Gamma-aminobutyric acid receptor subunit beta, RDL in complex with GABA and Abamectin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Apis mellifera (honey bee)

-
Macromolecule #1: Gamma-aminobutyric acid receptor subunit beta

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Apis mellifera (honey bee)
Molecular weightTheoretical: 53.517445 KDa
Recombinant expressionOrganism: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
SequenceString: MSFHAASWSF ALLAATVALL PATHRAPFAQ AATGGGSMLN DVNISAILDS FSVSYDKRVR PNYGGPPVEV GVTMYVLSIS SLSEVKMDF TLDFYFRQFW TDPRLAFKKR TGVETLSVGS EFIKNIWVPD TFFVNEKQSY FHIATTSNEF IRIHHSGSIT R SIRLTITA ...String:
MSFHAASWSF ALLAATVALL PATHRAPFAQ AATGGGSMLN DVNISAILDS FSVSYDKRVR PNYGGPPVEV GVTMYVLSIS SLSEVKMDF TLDFYFRQFW TDPRLAFKKR TGVETLSVGS EFIKNIWVPD TFFVNEKQSY FHIATTSNEF IRIHHSGSIT R SIRLTITA SCPMNLQYFP MDRQLCHIEI ESFGYTMRDI RYKWNEGPNS VGVSNEVSLP QFKVLGHRQR AMEISLTTGN YS RLACEIQ FVRSMGYYLI QIYIPSGLIV IISWVSFWLN RNATPARVAL GVTTVLTMTT LMSSTNAALP KISYVKSIDV YLG TCFVMV FASLLEYATV GYMAKRIQMR KNRFQKIAES MKTARENPGP PGVPGDHGDH APKQTVRFKV HDPKAHSKGG TLEN TINGR ADEEAAPAPQ HLIHPGKDIN KLYGMTPSDI DKYSRIVFPV CFVCFNLMYW IIYLHISDVV ADDLVLLEEA K

UniProtKB: Gamma-aminobutyric acid receptor subunit beta

-
Macromolecule #2: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 2 / Number of copies: 5 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID / neurotransmitter, inhibitor*YM

-
Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Macromolecule #4: Abamectin

MacromoleculeName: Abamectin / type: ligand / ID: 4 / Number of copies: 5 / Formula: A1JNZ
Molecular weightTheoretical: 873.077 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.86 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30111
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more