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- EMDB-52314: a5b3 GABAAR bound to GABA and Mb25 in a desensitized state in sap... -

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Basic information

Entry
Database: EMDB / ID: EMD-52314
Titlea5b3 GABAAR bound to GABA and Mb25 in a desensitized state in saposin nanodiscs after long GABA treatment
Map dataa5b3 GABAAR bound to GABA and Mb25 in desensitized state in saposin nanodisc with long GABA treatment
Sample
  • Complex: heteromeric assembly of 2 a5 and 3 b3 bound to 1 Mb25
    • 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
    • Protein or peptide: Megabody 25
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
  • 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 / Signaling by ERBB4 / associative learning / 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 / chloride transmembrane transport / cytoplasmic vesicle membrane / 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) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsCowgill J / Fan C / Howard RJ / Lindahl E
Funding support Sweden, European Union, 2 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
European Molecular Biology Organization (EMBO)ALTF 542-2021European Union
CitationJournal: To Be Published
Title: a5b3 GABAAR bound to GABA and Mb25 in a desensitized state in saposin nanodiscs after long GABA treatment
Authors: Cowgill J / Fan C / Howard RJ / Lindahl E
History
DepositionDec 11, 2024-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52314.png

Downloads & links

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Map

FileDownload / File: emd_52314.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationa5b3 GABAAR bound to GABA and Mb25 in desensitized state in saposin nanodisc with long GABA treatment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.65 Å/pix.
x 440 pix.
= 285.12 Å		0.65 Å/pix.
x 440 pix.
= 285.12 Å		0.65 Å/pix.
x 440 pix.
= 285.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.05
Minimum - Maximum-23.578878 - 37.498443999999999
Average (Standard dev.)0.000000000001258 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 285.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: unfiltered half map 1

Fileemd_52314_half_map_1.map
Annotationunfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: unfiltered half map 2

Fileemd_52314_half_map_2.map
Annotationunfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : heteromeric assembly of 2 a5 and 3 b3 bound to 1 Mb25

EntireName: heteromeric assembly of 2 a5 and 3 b3 bound to 1 Mb25
Components
  • Complex: heteromeric assembly of 2 a5 and 3 b3 bound to 1 Mb25
    • 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
    • Protein or peptide: Megabody 25
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: heteromeric assembly of 2 a5 and 3 b3 bound to 1 Mb25

SupramoleculeName: heteromeric assembly of 2 a5 and 3 b3 bound to 1 Mb25 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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 #3: Megabody 25

MacromoleculeName: Megabody 25 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 58.275121 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKKIWLALAG LVLAFSASAQ VQLVESGGGL VQTKTTTSVI DTTNDAQNLL TQAQTIVNTL KDYCPILIAK SSSSNGGTNN ANTPSWQTA GGGKNSCATF GAEFSAASDM INNAQKIVQE TQQLSANQPK NITQPHNLNL NSPSSLTALA QKMLKNAQSQ A EILKLANQ ...String:
MKKIWLALAG LVLAFSASAQ VQLVESGGGL VQTKTTTSVI DTTNDAQNLL TQAQTIVNTL KDYCPILIAK SSSSNGGTNN ANTPSWQTA GGGKNSCATF GAEFSAASDM INNAQKIVQE TQQLSANQPK NITQPHNLNL NSPSSLTALA QKMLKNAQSQ A EILKLANQ VESDFNKLSS GHLKDYIGKC DASAISSANM TMQNQKNNWG NGCAGVEETQ SLLKTSAADF NNQTPQINQA QN LANTLIQ ELGNNTYEQL SRLLTNDNGT NSKTSAQAIN QAVNNLNERA KTLAGGTTNS PAYQATLLAL RSVLGLWNSM GYA VICGGY TKSPGENNQK DFHYTDENGN GTTINCGGST NSNGTHSYNG TNTLKADKNV SLSIEQYEKI HEAYQILSKA LKQA GLAPL NSKGEKLEAH VTTSKYGSLR LSCAASGHTF NYPIMGWFRQ APGKEREFVG AISWSGGSTS YADSVKDRFT ISRDN AKNT VYLEMNNLKP EDTAVYYCAA KGRYSGGLYY PTNYDYWGQG TQVTVSSHHH HHHEPEA

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Macromolecule #10: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 10 / Number of copies: 2 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID

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Macromolecule #11: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

MacromoleculeName: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / type: ligand / ID: 11 / 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 #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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
2.0 mMGABA
20.0 mMHEPES
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K
Detailssample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 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: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Final refinement performed with Blush regularization
Number images used: 161171
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
DetailsInitial rigid body fit in ChimeraX followed by refinement with Isolde then Phenix
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9hns:
a5b3 GABAAR bound to GABA and Mb25 in a desensitized state in saposin nanodiscs after long GABA treatment

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