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- EMDB-50341: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-50341
TitleCryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state
Map dataUnsharpened map
Sample
  • Complex: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: HISTAMINE
  • Ligand: DECANE
  • Ligand: CHLORIDE ION
  • Ligand: water
KeywordsGABA / neurotransmission / gating cycle / time-resolved cryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / synaptic transmission, GABAergic / roof of mouth development ...cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / synaptic transmission, GABAergic / roof of mouth development / Signaling by ERBB4 / chloride channel complex / cytoplasmic vesicle membrane / chloride transmembrane transport / dendritic spine / postsynaptic membrane / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsMihaylov DB / Malinauskas T / Aricescu AR
Funding support United Kingdom, United States, 6 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
Cancer Research UKDRCRPG-May23/100002 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_EX_MR/T046279/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01-GM135550 United States
National Science Foundation (NSF, United States)NeuroNex 2014862 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state
Authors: Mihaylov DB / Malinauskas T / Aricescu AR
History
DepositionMay 21, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50341.png

Downloads & links

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Map

FileDownload / File: emd_50341.map.gz / Format: CCP4 / Size: 120.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 316 pix.
= 260.384 Å		0.82 Å/pix.
x 316 pix.
= 260.384 Å		0.82 Å/pix.
x 316 pix.
= 260.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.015365541 - 0.049798705
Average (Standard dev.)-0.00015772443 (±0.0018615962)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions316316316
Spacing316316316
CellA=B=C: 260.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50341_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_50341_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the half maps

Fileemd_50341_half_map_1.map
AnnotationOne of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the half maps

Fileemd_50341_half_map_2.map
AnnotationOne of the half maps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the beta3 homomeric GABA(A) receptor in comp...

EntireName: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state
Components
  • Complex: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: HISTAMINE
  • Ligand: DECANE
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in comp...

SupramoleculeName: Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 250 KDa

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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: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.643246 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPDY DIPTTENLYF QGTGQSVNDP GNMSFVKETV DKLLKGYDIR LRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQQ YWRDKRLAYS GIPLNLTLDN RVADQLWVPD TYFLNDKKSF V HGVTVKNR ...String:
MDEKTTGWRG GHVVEGLAGE LEQLRARLEH HPQGQREPDY DIPTTENLYF QGTGQSVNDP GNMSFVKETV DKLLKGYDIR LRPDFGGPP VCVGMNIDIA SIDMVSEVNM DYTLTMYFQQ YWRDKRLAYS GIPLNLTLDN RVADQLWVPD TYFLNDKKSF V HGVTVKNR MIRLHPDGTV LYGLRITTTA ACMMDLRRYP LDEQNCTLEI ESYGYTTDDI EFYWRGGDKA VTGVERIELP QF SIVEHRL VSRNVVFATG AYPRLSLSFR LKRNIGYFIL QTYMPSILIT ILSWVSFWIN YDASAARVAL GITTVLTMTT INT HLRETL PKIPYVKAID MYLMGCFVFV FLALLEYAFV NYIFFSQPAR AAAIDRWSRI VFPFTFSLFN LVYWLYYVN

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3, Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: HISTAMINE

MacromoleculeName: HISTAMINE / type: ligand / ID: 5 / Number of copies: 5 / Formula: HSM
Molecular weightTheoretical: 111.145 Da
Chemical component information

ChemComp-HSM:
HISTAMINE / neurotransmitter, hormone*YM

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Macromolecule #6: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 6 / Number of copies: 15 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #7: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 370 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
4.3 mMNa2HPODisodium phosphate

Details: 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: current: 30mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 20757 / Average exposure time: 6.43 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8401972
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 91000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7a5v


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 30 / Target criteria: FSC at 0.5
Output model

PDB-9feu:
Cryo-EM structure of the beta3 homomeric GABA(A) receptor in complex with HSM in the long-lived symmetric desensitised state

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