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- EMDB-4411: Cryo-EM structure of the human synaptic alpha1-beta3-gamma2 GABAA... -

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Basic information

Entry
Database: EMDB / ID: EMD-4411
TitleCryo-EM structure of the human synaptic alpha1-beta3-gamma2 GABAA receptor in complex with Megabody38 in a lipid nanodisc
Map dataCryo-EM map of a GABAA receptor in lipid nanodisc
Sample
  • Complex: Human alpha1-beta3-gamma2 GABA-A receptor in complex with Megabody38 and in lipid nanodiscs
    • Complex: Human alpha1-beta3-gamma2 GABA-A receptor
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Complex: Megabody38
      • Protein or peptide: Megabody38
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
Function / homology
Function and homology information


benzodiazepine receptor activity / GABA receptor complex / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / cellular response to histamine / GABA-gated chloride ion channel activity / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / neurotransmitter receptor activity ...benzodiazepine receptor activity / GABA receptor complex / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / cellular response to histamine / GABA-gated chloride ion channel activity / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / neurotransmitter receptor activity / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / adult behavior / chloride channel activity / roof of mouth development / Signaling by ERBB4 / chloride channel complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / chloride transmembrane transport / dendrite membrane / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / postsynaptic membrane / postsynapse / neuron projection / axon / synapse / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / : / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. ...Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / : / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / : / Gamma-aminobutyric-acid A receptor, alpha 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 alpha-1 / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLaverty D / Desai R / Uchanski T / Masiulis S / Wojciech JS / Malinauskas T / Zivanov J / Pardon E / Steyaert J / Miller KW / Aricescu AR
Funding support United Kingdom, Switzerland, United States, 7 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (United Kingdom)MC_UP_1201/15 United Kingdom
Medical Research Council (United Kingdom)MC_UP_A025_1013 United Kingdom
Human Frontier Science ProgramRGP0065/2014 United Kingdom
Cancer Research UKC20724/A14414 United Kingdom
Swiss National Science Foundation168735 Switzerland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 58448 United States
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structure of the human α1β3γ2 GABA receptor in a lipid bilayer.
Authors: Duncan Laverty / Rooma Desai / Tomasz Uchański / Simonas Masiulis / Wojciech J Stec / Tomas Malinauskas / Jasenko Zivanov / Els Pardon / Jan Steyaert / Keith W Miller / A Radu Aricescu /
Abstract: Type A γ-aminobutyric acid (GABA) receptors are pentameric ligand-gated ion channels and the main drivers of fast inhibitory neurotransmission in the vertebrate nervous system. Their dysfunction is ...Type A γ-aminobutyric acid (GABA) receptors are pentameric ligand-gated ion channels and the main drivers of fast inhibitory neurotransmission in the vertebrate nervous system. Their dysfunction is implicated in a range of neurological disorders, including depression, epilepsy and schizophrenia. Among the numerous assemblies that are theoretically possible, the most prevalent in the brain are the α1β2/3γ2 GABA receptors. The β3 subunit has an important role in maintaining inhibitory tone, and the expression of this subunit alone is sufficient to rescue inhibitory synaptic transmission in β1-β3 triple knockout neurons. So far, efforts to generate accurate structural models for heteromeric GABA receptors have been hampered by the use of engineered receptors and the presence of detergents. Notably, some recent cryo-electron microscopy reconstructions have reported 'collapsed' conformations; however, these disagree with the structure of the prototypical pentameric ligand-gated ion channel the Torpedo nicotinic acetylcholine receptor, the large body of structural work on homologous homopentameric receptor variants and the logic of an ion-channel architecture. Here we present a high-resolution cryo-electron microscopy structure of the full-length human α1β3γ2L-a major synaptic GABA receptor isoform-that is functionally reconstituted in lipid nanodiscs. The receptor is bound to a positive allosteric modulator 'megabody' and is in a desensitized conformation. Each GABA receptor pentamer contains two phosphatidylinositol-4,5-bisphosphate molecules, the head groups of which occupy positively charged pockets in the intracellular juxtamembrane regions of α1 subunits. Beyond this level, the intracellular M3-M4 loops are largely disordered, possibly because interacting post-synaptic proteins are not present. This structure illustrates the molecular principles of heteromeric GABA receptor organization and provides a reference framework for future mechanistic investigations of GABAergic signalling and pharmacology.
History
DepositionNov 12, 2018-
Header (metadata) releaseDec 26, 2018-
Map releaseJan 2, 2019-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6i53
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4411.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of a GABAA receptor in lipid nanodisc
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.14780992 - 0.22108346
Average (Standard dev.)0.00032399263 (±0.0058954824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1480.2210.000

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Supplemental data

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Mask #1

Fileemd_4411_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_4411_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_4411_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Human alpha1-beta3-gamma2 GABA-A receptor in complex with Megabod...

EntireName: Human alpha1-beta3-gamma2 GABA-A receptor in complex with Megabody38 and in lipid nanodiscs
Components
  • Complex: Human alpha1-beta3-gamma2 GABA-A receptor in complex with Megabody38 and in lipid nanodiscs
    • Complex: Human alpha1-beta3-gamma2 GABA-A receptor
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Complex: Megabody38
      • Protein or peptide: Megabody38
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Supramolecule #1: Human alpha1-beta3-gamma2 GABA-A receptor in complex with Megabod...

SupramoleculeName: Human alpha1-beta3-gamma2 GABA-A receptor in complex with Megabody38 and in lipid nanodiscs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 400 KDa

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Supramolecule #2: Human alpha1-beta3-gamma2 GABA-A receptor

SupramoleculeName: Human alpha1-beta3-gamma2 GABA-A receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant strain: Embryonic kidney cells

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Supramolecule #3: Megabody38

SupramoleculeName: Megabody38 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Gamma-aminobutyric acid receptor subunit beta-3

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.444578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MCSGLLELLL PIWLSWTLGT RGSEPRSVND PGNMSFVKET VDKLLKGYDI RLRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQ QYWRDKRLAY SGIPLNLTLD NRVADQLWVP DTYFLNDKKS FVHGVTVKNR MIRLHPDGTV LYGLRITTTA A CMMDLRRY ...String:
MCSGLLELLL PIWLSWTLGT RGSEPRSVND 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 VNYIFFGRGP QRQKKLAEKT AKAKNDRSKS ESNRVDAHGN ILLTSLEVHN EMNEVSGGIG DTRNSAISFD NSGI QYRKQ SMPREGHGRF LGDRSLPHKK THLRRRSSQL KIKIPDLTDV NAIDRWSRIV FPFTFSLFNL VYWLYYVN

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Macromolecule #2: Gamma-aminobutyric acid receptor subunit alpha-1

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.916602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKKSPGLSDY LWAWTLFLST LTGRSYGDYK DDDDKQPSLQ DELKDNTTVF TRILDRLLDG YDNRLRPGLG ERVTEVKTDI FVTSFGPVS DHDMEYTIDV FFRQSWKDER LKFKGPMTVL RLNNLMASKI WTPDTFFHNG KKSVAHNMTM PNKLLRITED G TLLYTMRL ...String:
MKKSPGLSDY LWAWTLFLST LTGRSYGDYK DDDDKQPSLQ DELKDNTTVF TRILDRLLDG YDNRLRPGLG ERVTEVKTDI FVTSFGPVS DHDMEYTIDV FFRQSWKDER LKFKGPMTVL RLNNLMASKI WTPDTFFHNG KKSVAHNMTM PNKLLRITED G TLLYTMRL TVRAECPMHL EDFPMDAHAC PLKFGSYAYT RAEVVYEWTR EPARSVVVAE DGSRLNQYDL LGQTVDSGIV QS STGEYVV MTTHFHLKRK IGYFVIQTYL PCIMTVILSQ VSFWLNRESV PARTVFGVTT VLTMTTLSIS ARNSLPKVAY ATA MDWFIA VCYAFVFSAL IEFATVNYFT KRGYAWDGKS VVPEKPKKVK DPLIKKNNTY APTATSYTPN LARGDPGLAT IAKS ATIEP KEVKPETKPP EPKKTFNSVS KIDRLSRIAF PLLFGIFNLV YWATYLNREP QLKAPTPHQ

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Macromolecule #3: Gamma-aminobutyric acid receptor subunit gamma-2

MacromoleculeName: Gamma-aminobutyric acid receptor subunit gamma-2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.922055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSPNIWSTG SSVYSTPVFS QKMTVWILLL LSLYPGFTSQ KSDDDYEDYA SNKTWVLTPK VPEGDVTVIL NNLLEGYDNK LRPDIGVKP TLIHTDMYVN SIGPVNAINM EYTIDIFFAQ TWYDRRLKFN STIKVLRLNS NMVGKIWIPD TFFRNSKKAD A HWITTPNR ...String:
MSSPNIWSTG SSVYSTPVFS QKMTVWILLL LSLYPGFTSQ KSDDDYEDYA SNKTWVLTPK VPEGDVTVIL NNLLEGYDNK LRPDIGVKP TLIHTDMYVN SIGPVNAINM EYTIDIFFAQ TWYDRRLKFN STIKVLRLNS NMVGKIWIPD TFFRNSKKAD A HWITTPNR MLRIWNDGRV LYTLRLTIDA ECQLQLHNFP MDEHSCPLEF SSYGYPREEI VYQWKRSSVE VGDTRSWRLY QF SFVGLRN TTEVVKTTSG DYVVMSVYFD LSRRMGYFTI QTYIPCTLIV VLSWVSFWIN KDAVPARTSL GITTVLTMTT LST IARKSL PKVSYVTAMD LFVSVCFIFV FSALVEYGTL HYFVSNRKPS KDKDKKKKNP LLRMFSFKAP TIDIRPRSAT IQMN NATHL QERDEEYGYE CLDGKDCASF FCCFEDCRTG AWRHGRIHIR IAKMDSYARI FFPTAFCLFN LVYWVSYLYL GGSGG SGGS GKTETSQVAP A

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Macromolecule #4: Megabody38

MacromoleculeName: Megabody38 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.462909 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRV SCAASGRTFT AYIMAWFRQA PGKEREFLAA MDQGRIQYYG DSVRGRFTIS RDYAKNSVDL QLDGLRPED TAVYYCAAGA GFWGLRTASS YHYWGQGTQV TVSS

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Macromolecule #9: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 9 / Number of copies: 3 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM / POPC

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Macromolecule #10: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 10 / Number of copies: 2 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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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

Concentration0.5 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chlorideSodium chloride
10.0 mMC8H18N2O4SHEPES
GridModel: Quantifoil, UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 287.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe purified receptor-nanodisc complex was mixed with Mb38 prior to grid preparation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 0.7000000000000001 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.7000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 75000
Specialist opticsPhase plate: VOLTA PHASE PLATE
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 784 / Average exposure time: 60.0 sec. / Average electron dose: 30.84 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. v1.18)
Details: CTF parameters were estimated using GCTF and CTF correction performed in RELION (full phase and amplitude correction).
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Version: RELION
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. v3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Version: RELION
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 55449

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6i53:
Cryo-EM structure of the human synaptic alpha1-beta3-gamma2 GABAA receptor in complex with Megabody38 in a lipid nanodisc

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