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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: 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
SampleHuman alpha1-beta3-gamma2 GABA-A receptor in complex with Megabody38 and in lipid nanodiscs
  • Human alpha1-beta3-gamma2 GABA-A receptor
  • (Megabody38) x 2
  • (Gamma-aminobutyric acid receptor subunit ...) x 3
  • (ligand) x 5
Function / homologyNeurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric-acid A receptor, gamma subunit / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel / Gamma-aminobutyric-acid A receptor, alpha subunit / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric-acid A receptor, gamma subunit / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel / Gamma-aminobutyric-acid A receptor, alpha subunit / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channels signature. / GABA A receptor activation / GABA receptor activation / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / benzodiazepine receptor activity / inner ear receptor cell development / inhibitory extracellular ligand-gated ion channel activity / GABA-A receptor complex / GABA receptor complex / GABA-A receptor activity / GABA-gated chloride ion channel activity / regulation of postsynaptic membrane potential / cellular response to histamine / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / innervation / integral component of postsynaptic specialization membrane / inhibitory postsynaptic potential / chloride channel activity / adult behavior / chloride channel complex / chloride transmembrane transport / cochlea development / dendrite membrane / GABA-ergic synapse / nervous system process / roof of mouth development / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / ion transmembrane transport / regulation of membrane potential / post-embryonic development / sensory perception of sound / cytoplasmic vesicle membrane / postsynapse / postsynaptic membrane / chemical synaptic transmission / drug binding / negative regulation of neuron apoptotic process / cell junction / neuron projection / synapse / axon / integral component of plasma membrane / signal transduction / identical protein binding / plasma membrane / Gamma-aminobutyric acid receptor subunit alpha-1 / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit beta-3
Function and homology information
SourceHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsLaverty D / Desai R / Uchanski T / Masiulis S / Wojciech JS / Malinauskas T / Zivanov J / Pardon E / Steyaert J / Miller KW / Aricescu AR
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
Validation ReportPDB-ID: 6i53

SummaryFull reportAbout validation report
DateDeposition: Nov 12, 2018 / Header (metadata) release: Dec 26, 2018 / Map release: Jan 2, 2019 / Last update: Jan 16, 2019

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Structure visualization

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

Downloads & links

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Map

Fileemd_4411.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.07 Å/pix.
= 273.92 Å
256 pix
1.07 Å/pix.
= 273.92 Å
256 pix
1.07 Å/pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.14780992 - 0.22108346
Average (Standard dev.)0.00032399263 (0.0058954824)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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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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
Number of components: 12

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Component #1: protein, Human alpha1-beta3-gamma2 GABA-A receptor in complex wit...

ProteinName: Human alpha1-beta3-gamma2 GABA-A receptor in complex with Megabody38 and in lipid nanodiscs
Recombinant expression: No
MassTheoretical: 400 kDa

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Component #2: protein, Human alpha1-beta3-gamma2 GABA-A receptor

ProteinName: Human alpha1-beta3-gamma2 GABA-A receptor / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Strain: Embryonic kidney cells

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Component #3: protein, Megabody38

ProteinName: Megabody38 / Recombinant expression: No
SourceSpecies: Lama glama (llama)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Gamma-aminobutyric acid receptor subunit beta-3

ProteinName: Gamma-aminobutyric acid receptor subunit beta-3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 54.444578 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Gamma-aminobutyric acid receptor subunit alpha-1

ProteinName: Gamma-aminobutyric acid receptor subunit alpha-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 52.916602 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, Gamma-aminobutyric acid receptor subunit gamma-2

ProteinName: Gamma-aminobutyric acid receptor subunit gamma-2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.922055 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, Megabody38

ProteinName: Megabody38 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.462909 kDa
SourceSpecies: Lama glama (llama)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 14 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #10: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 11 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #11: ligand, (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propy...

LigandName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.760076 kDa

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Component #12: ligand, [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,...

LigandName: [(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
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.746566 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.5 mg/ml / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 287.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 30.84 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal), 75000.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 700.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 784

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 55449
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION
CTF correction: CTF parameters were estimated using GCTF and CTF correction performed in RELION (full phase and amplitude correction).
Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Output model

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