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- EMDB-51980: a5b3 GABAA Receptor resting state -

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Basic information

Entry
Database: EMDB / ID: EMD-51980
Titlea5b3 GABAA Receptor resting state
Map datasharpened map of resting a5b3 GABAA receptor
Sample
  • Complex: a5b3 GABAA receptor in resting state bound to zinc and butyrate
    • Protein or peptide: Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein
  • Ligand: butanoic acid
  • Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGABA receptor / pentameric ligand gated ion channel / cys-loop receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


circadian sleep/wake cycle, REM sleep / reproductive behavior / GABA receptor binding / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity ...circadian sleep/wake cycle, REM sleep / reproductive behavior / GABA receptor binding / hard palate development / cellular response to histamine / GABA receptor activation / inner ear receptor cell development / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / innervation / response to anesthetic / postsynaptic specialization membrane / neuronal cell body membrane / inhibitory postsynaptic potential / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / cellular response to zinc ion / exploration behavior / motor behavior / roof of mouth development / associative learning / Signaling by ERBB4 / cochlea development / social behavior / chloride channel complex / behavioral fear response / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoplasmic vesicle membrane / chloride transmembrane transport / bioluminescence / cerebellum development / learning / generation of precursor metabolites and energy / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / memory / signaling receptor activity / presynaptic membrane / dendritic spine / postsynaptic membrane / postsynapse / response to xenobiotic stimulus / cell surface / signal transduction / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, alpha subunit / : / 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 ...Gamma-aminobutyric-acid A receptor, alpha 5 subunit / Gamma-aminobutyric-acid A receptor, alpha subunit / : / 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 / Green fluorescent protein, GFP / 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 / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit beta-3 / Gamma-aminobutyric acid receptor subunit alpha-5 / Green fluorescent protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsCowgill J / Fan C / Howard RJ / Lindahl E
Funding supportEuropean Union, Sweden, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 542-2021European Union
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: Structural basis for activation and potentiation in a human a5b3 GABAA receptor
Authors: Cowgill J / Fan C / Howard RJ / Lindahl E
History
DepositionNov 2, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51980.png

Downloads & links

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Map

FileDownload / File: emd_51980.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map of resting a5b3 GABAA receptor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.65 Å/pix.
x 440 pix.
= 286. Å		0.65 Å/pix.
x 440 pix.
= 286. Å		0.65 Å/pix.
x 440 pix.
= 286. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5
Minimum - Maximum-25.209309000000001 - 39.450629999999997
Average (Standard dev.)0.000000000003969 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 286.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: unfiltered half map 2

Fileemd_51980_half_map_1.map
Annotationunfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map 1

Fileemd_51980_half_map_2.map
Annotationunfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : a5b3 GABAA receptor in resting state bound to zinc and butyrate

EntireName: a5b3 GABAA receptor in resting state bound to zinc and butyrate
Components
  • Complex: a5b3 GABAA receptor in resting state bound to zinc and butyrate
    • Protein or peptide: Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein
  • Ligand: butanoic acid
  • Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
  • Ligand: ZINC ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: a5b3 GABAA receptor in resting state bound to zinc and butyrate

SupramoleculeName: a5b3 GABAA receptor in resting state bound to zinc and butyrate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Green fluorescent protein,Gamma-aminobutyric acid receptor subuni...

MacromoleculeName: Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.207281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRKSPGLSDC LWAWILLLST LTGRSYGQMS KGEELFTGVV PILVELDGDV NGHKFSVRGE GEGDATNGKL TLKFICTTGK LPVPWPTLV TTLTYGVQCF SRYPDHMKRH DFFKSAMPEG YVQERTISFK DDGTYKTRAE VKFEGDTLVN RIELKGIDFK E DGNILGHK ...String:
MRKSPGLSDC LWAWILLLST LTGRSYGQMS KGEELFTGVV PILVELDGDV NGHKFSVRGE GEGDATNGKL TLKFICTTGK LPVPWPTLV TTLTYGVQCF SRYPDHMKRH DFFKSAMPEG YVQERTISFK DDGTYKTRAE VKFEGDTLVN RIELKGIDFK E DGNILGHK LEYNFNSHNV YITADKQKNG IKANFKIRHN VEDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSVLSKD PN EKRDHMV LLEFVTAAGI THGMDELYKA ANALAAWSHP QFEKGGGSGG GSGGGSWSHP QFEKSSSNNN NNENLYFQAM PTS SVKDET NDNITIFTRI LDGLLDGYDN RLRPGLGERI TQVRTDIYVT SFGPVSDTEM EYTIDVFFRQ SWKDERLRFK GPMQ RLPLN NLLASKIWTP DTFFHNGKKS IAHNMTTPNK LLRLEDDGTL LYTMRLTISA ECPMQLEDFP MDAHACPLKF GSYAY PNSE VVYVWTNGST KSVVVAEDGS RLNQYHLMGQ TVGTENISTS TGEYTIMTAH FHLKRKIGYF VIQTYLPCIM TVILSQ VSF WLNRESVPAR TVFGVTTVLT MTTLSISARN SLPKVAYATA MDWFIAVCYA FVFSALIEFA TVNYFTKSQP ARAASIS KI DKMSRIVFPV LFGTFNLVYW ATYLNREPVI KGAASPK

UniProtKB: Green fluorescent protein, Gamma-aminobutyric acid receptor subunit alpha-5, Gamma-aminobutyric acid receptor subunit alpha-5

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Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent...

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 71.07343 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWGLAGGRLF GIFSAPVLVA VVCCAQSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY ...String:
MWGLAGGRLF GIFSAPVLVA VVCCAQSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY PLDEQNCTLE IESYGYTTDD IEFYWRGGDK AVTGVERIEL PQFSIVEHRL VSRNVVFATG AYPRLSLSFR LK RNIGYFI LQTYMPSILI TILSWVSFWI NYDASAARVA LGITTVLTMT TINTHLRETL PKIPYVKAID MYLMGCFVFV FLA LLEYAF VNYIFFSQPG RAMVSKGEEL FTGVVPILVE MDGDVNGRKF SVRGVGEGDA THGKLTLKFI CTSGKLPVPW PTLV TTLSY GVQCFSRYPD HMKQHDFFKS AMPEGYVQER TIFFKDDGSY KTRAEVKFEG DTLVNRIVLK GTDFKEDGNI LGHKL EYNM NVGNVYITAD KQKNGIKANF EIRHNVEDGG VQLADHYQQN TPIGDGSVLL PDNHYLSVQV KLSKDPNEKR DHMVLL EFR TAAGITPGMD ELYKGRAAAI DRWSRIVFPF TFSLFNLVYW LYYVNSRENL YFQAHHHHHH

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3, Green fluorescent protein, Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #9: butanoic acid

MacromoleculeName: butanoic acid / type: ligand / ID: 9 / Number of copies: 2 / Formula: BUA
Molecular weightTheoretical: 88.105 Da
Chemical component information

ChemComp-BUA:
butanoic acid

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Macromolecule #10: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

MacromoleculeName: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / type: ligand / ID: 10 / Number of copies: 1 / Formula: EPE
Molecular weightTheoretical: 238.305 Da
Chemical component information

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM

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Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 1 / 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

Concentration4.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
20.0 mMHEPES

Details: 20 mM HEPES, 100 mM NaCl, 2 mM Fluorinated Fos-choline 8, 0.005% LMNG, 0.0005% CHS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was monodisprese and prepared

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 58.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68589
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9haa:
a5b3 GABAA Receptor resting state

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