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- EMDB-50712: CryoEM structure of human rho1 GABAA receptor in complex with THIP -

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Basic information

Entry
Database: EMDB / ID: EMD-50712
TitleCryoEM structure of human rho1 GABAA receptor in complex with THIP
Map data
Sample
  • Complex: human rho1 GABAA receptor
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit rho-1
  • Ligand: 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: HEXANE
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: CHLORIDE ION
  • Ligand: water
KeywordsIon channel / TRANSLOCASE
Function / homology
Function and homology information


GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / gamma-aminobutyric acid signaling pathway / intracellular vesicle / chloride channel complex / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / chloride transmembrane transport / GABA-ergic synapse ...GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / gamma-aminobutyric acid signaling pathway / intracellular vesicle / chloride channel complex / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / chloride transmembrane transport / GABA-ergic synapse / modulation of chemical synaptic transmission / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / protein domain specific binding / protein-containing complex binding / glutamatergic synapse / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, Rho / Gamma-aminobutyric-acid A receptor, Rho1 / 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 ...Gamma-aminobutyric-acid A receptor, Rho / Gamma-aminobutyric-acid A receptor, Rho1 / 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 rho-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.19 Å
AuthorsFan C / Howard RJ / Lindahl E
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2019-02433 Sweden
CitationJournal: To Be Published
Title: Cryo-EM structures of Rho1 GABAA receptors with antagonist and agonist drugs
Authors: Fan C / Cowgill J / Howard RJ / Lindahl E
History
DepositionJun 18, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50712.png

Downloads & links

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Map

FileDownload / File: emd_50712.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 420 pix.
= 282.45 Å		0.67 Å/pix.
x 420 pix.
= 282.45 Å		0.67 Å/pix.
x 420 pix.
= 282.45 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.8859303 - 1.5598775
Average (Standard dev.)0.0015320127 (±0.039337333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 282.45 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50712_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50712_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human rho1 GABAA receptor

EntireName: human rho1 GABAA receptor
Components
  • Complex: human rho1 GABAA receptor
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit rho-1
  • Ligand: 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: HEXANE
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: human rho1 GABAA receptor

SupramoleculeName: human rho1 GABAA receptor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Gamma-aminobutyric acid receptor subunit rho-1

MacromoleculeName: Gamma-aminobutyric acid receptor subunit rho-1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.95023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLAVPNMRFG IFLLWWGWVL ATESRMHWPG REVHEMSKKG RPQRQRREVH EDAHKQVSPI LRRSPDITKS PLTKSEQLLR IDDHDFSMR PGFGGPAIPV GVDVQVESLD SISEVDMDFT MTLYLRHYWK DERLSFPSTN NLSMTFDGRL VKKIWVPDMF F VHSKRSFI ...String:
MLAVPNMRFG IFLLWWGWVL ATESRMHWPG REVHEMSKKG RPQRQRREVH EDAHKQVSPI LRRSPDITKS PLTKSEQLLR IDDHDFSMR PGFGGPAIPV GVDVQVESLD SISEVDMDFT MTLYLRHYWK DERLSFPSTN NLSMTFDGRL VKKIWVPDMF F VHSKRSFI HDTTTDNVML RVQPDGKVLY SLRVTVTAMC NMDFSRFPLD TQTCSLEIES YAYTEDDLML YWKKGNDSLK TD ERISLSQ FLIQEFHTTT KLAFYSSTGW YNRLYINFTL RRHIFFFLLQ TYFPATLMVM LSWVSFWIDR RAVPARVPLG ITT VLTMST IITGVNASMP RVSYIKAVDI YLWVSFVFVF LSVLEYAAVN YLTTVQERKE QKLREKLPCT SGLPPPRTAM LDGN YSDGE VNDLDNYMPE NGEKPDRMMV QLTLASERSS PQRKSQRSSY VSMRIDTHAI DKYSRIIFPA AYILFNLIYW SIFS

UniProtKB: Gamma-aminobutyric acid receptor subunit rho-1

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Macromolecule #2: 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one

MacromoleculeName: 4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one / type: ligand / ID: 2 / Number of copies: 5 / Formula: EI7
Molecular weightTheoretical: 140.14 Da
Chemical component information

ChemComp-EI7:
4,5,6,7-tetrahydro-[1,2]oxazolo[5,4-c]pyridin-3-one / alkaloid*YM

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 4 / Number of copies: 20 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #5: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 5 / Number of copies: 5 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #6: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 6 / Number of copies: 10 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #7: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 7 / Number of copies: 5 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #8: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 335 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135764
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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