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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


circadian sleep/wake cycle, REM sleep / reproductive behavior / 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 ...circadian sleep/wake cycle, REM sleep / reproductive behavior / 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 / 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 / cochlea development / social behavior / chloride channel complex / cytoplasmic vesicle membrane / chloride transmembrane transport / cerebellum development / learning / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / memory / dendritic spine / postsynaptic membrane / response to xenobiotic stimulus / cell surface / 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: Structure / Year: 2025
Title: Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV.
Authors: Dimple Karia / Adrian F Koh / Wen Yang / Victoria I Cushing / Benjamin Basanta / Daniel B Mihaylov / Sagar Khavnekar / Ondřej Vyroubal / Miloš Malínský / Ondřej Sháněl / Vojtěch ...Authors: Dimple Karia / Adrian F Koh / Wen Yang / Victoria I Cushing / Benjamin Basanta / Daniel B Mihaylov / Sagar Khavnekar / Ondřej Vyroubal / Miloš Malínský / Ondřej Sháněl / Vojtěch Doležal / Jürgen Plitzko / Lingbo Yu / Gabriel C Lander / A Radu Aricescu / Basil J Greber / Abhay Kotecha /
Abstract: Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report sub-3 Å resolution structures using the 100 keV ...Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report sub-3 Å resolution structures using the 100 keV Tundra cryo-TEM, equipped with the Falcon C direct electron detector (DED). This system combines advanced optics, extreme-brightness field emission gun (XFEG), and SP-TWIN lens to enhance coherence and resolution. The semi-automated loader reduced contamination and drift, enabling extended data collection, while the high detective quantum efficiency (DQE) of Falcon C improved signal-to-noise ratio. We validated performance by determining structures of biological samples, including apoferritin (2.1 Å), T20S proteasome (2.7 Å), GABA receptor (2.8 Å), hemoglobin (5.0 Å), transthyretin (3.5 Å), and AAV9 capsid (2.8 Å), spanning 50 kDa-3.9 MDa. This work highlights the potential of 100 keV transmission electron microscopes (TEMs) to make cryo-EM more accessible. It sets a precedent for using lower voltage TEMs not only for screening, but also for high-resolution protein structure determination.
History
DepositionNov 1, 2021-
Header (metadata) releaseFeb 2, 2022-
Map releaseFeb 2, 2022-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing 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
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13) / Type: NONE
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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