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- EMDB-13816: CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tund... -

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Basic information

Entry
Database: EMDB / ID: EMD-13816
TitleCryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope
Map dataCryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope
Sample
  • Complex: Human GABA(A)R-beta3 homopentamer
KeywordsIon channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


cellular response to histamine / GABA receptor activation / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / inhibitory synapse assembly / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / nervous system process / neurotransmitter receptor activity ...cellular response to histamine / GABA receptor activation / GABA-gated chloride ion channel activity / GABA-A receptor activity / GABA-A receptor complex / inhibitory synapse assembly / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / nervous system process / neurotransmitter receptor activity / roof of mouth development / Signaling by ERBB4 / chloride channel complex / transmembrane transporter complex / chloride transmembrane transport / regulation of membrane potential / cytoplasmic vesicle membrane / postsynaptic membrane / neuron projection / synapse / signal transduction / identical protein binding / plasma 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-3
Similarity search - Component
Biological speciesHEK 293S cells (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKaria D / Koh AF / Yu L / Kotecha A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Other private Netherlands
CitationJournal: To Be Published
Title: CryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope
Authors: Karia D / Koh AF / Yu L / Kotecha A
History
DepositionNov 1, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0815
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0815
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13816.png

Downloads & links

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Map

FileDownload / File: emd_13816.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of GABA(A)R-beta3 homopentamer at 3.4A from Tundra, 100kV microscope
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.5 Å/pix.
x 256 pix.
= 384.62 Å		1.5 Å/pix.
x 256 pix.
= 384.62 Å		1.5 Å/pix.
x 256 pix.
= 384.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.50242 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0815 / Movie #1: 0.0815
Minimum - Maximum-0.22748959 - 0.42289117
Average (Standard dev.)0.0004282167 (±0.0071593635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 384.6195 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5024218751.5024218751.502421875
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z384.620384.620384.620
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2270.4230.000

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Supplemental data

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Sample components

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Entire : Human GABA(A)R-beta3 homopentamer

EntireName: Human GABA(A)R-beta3 homopentamer
Components
  • Complex: Human GABA(A)R-beta3 homopentamer

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Supramolecule #1: Human GABA(A)R-beta3 homopentamer

SupramoleculeName: Human GABA(A)R-beta3 homopentamer / type: complex / ID: 1 / Parent: 0
Details: Human GABA(A)R-beta3 homopentamer in complex with Megabody-25 in lipid nanodisc
Source (natural)Organism: HEK 293S cells (E. coli)
Molecular weightTheoretical: 200 KDa

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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: 7.6
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 287 K / Instrument: LEICA PLUNGER

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Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 3952 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal magnification: 180000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 413168
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 92997
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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