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- EMDB-54929: Structure of the honeybee GABAA RDL receptor apo state -

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Basic information

Entry
Database: EMDB / ID: EMD-54929
TitleStructure of the honeybee GABAA RDL receptor apo state
Map data
Sample
  • Complex: Gamma-aminobutyric acid receptor subunit beta, RDL
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGABAA receptor / insect / neurotransmission / 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: 2.9 Å
AuthorsLaboure T / Nury H
Funding support France, 1 items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Structures of the honeybee GABAA RDL receptor illuminate allosteric modulation
Authors: Laboure T / Pandey MP / Zarkadas L / Juillan-Binard C / Baud D / Cens T / Rousset M / Dehez F / Charnet P / Nury H
History
DepositionAug 29, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54929.png

Downloads & links

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Map

FileDownload / File: emd_54929.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.)
1.15 Å/pix.
x 320 pix.
= 366.4 Å		1.15 Å/pix.
x 320 pix.
= 366.4 Å		1.15 Å/pix.
x 320 pix.
= 366.4 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.145 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-0.4274311 - 1.0812358
Average (Standard dev.)0.000035302335 (±0.018616464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 366.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54929_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_54929_additional_1.map
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Half map: #2

Fileemd_54929_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_54929_half_map_2.map
Projections & Slices
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Histogram

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Sample components

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Entire : Gamma-aminobutyric acid receptor subunit beta, RDL

EntireName: Gamma-aminobutyric acid receptor subunit beta, RDL
Components
  • Complex: Gamma-aminobutyric acid receptor subunit beta, RDL
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Gamma-aminobutyric acid receptor subunit beta, RDL

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

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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

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54629
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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