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- EMDB-19173: CryoEM structure of human rho1 GABAA receptor in complex with pre... -

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Basic information

Entry
Database: EMDB / ID: EMD-19173
TitleCryoEM structure of human rho1 GABAA receptor in complex with pregnenolone sulfate
Map data
Sample
  • Complex: human rho1 GABAA receptor in complex with estradiol
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit rho-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: HEXANE
  • Ligand: Pregnenolone sulfate
  • Ligand: CHLORIDE ION
  • Ligand: water
KeywordsComplex / MEMBRANE PROTEIN
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 / neurotransmitter receptor activity / chloride channel complex / transmembrane transporter complex / GABA-ergic synapse / chloride transmembrane transport ...GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / gamma-aminobutyric acid signaling pathway / neurotransmitter receptor activity / chloride channel complex / transmembrane transporter complex / GABA-ergic synapse / chloride transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / modulation of chemical synaptic transmission / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / neuron projection / protein domain specific binding / glutamatergic synapse / synapse / protein-containing complex binding / 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, 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 ...Gamma-aminobutyric-acid A receptor, Rho / Gamma-aminobutyric-acid A receptor, Rho1 / 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 rho-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsChen F / John C / Rebecca JH / Erik L
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Nat Commun / Year: 2024
Title: Divergent mechanisms of steroid inhibition in the human rho1 GABAA receptor
Authors: Chen F / John C / Rebecca JH / Erik L
History
DepositionDec 15, 2023-
Header (metadata) releaseAug 28, 2024-
Map releaseAug 28, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19173.png

Downloads & links

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Map

FileDownload / File: emd_19173.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-0.3925328 - 0.68674374
Average (Standard dev.)0.0011529721 (±0.018832767)
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_19173_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_19173_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 in complex with estradiol

EntireName: human rho1 GABAA receptor in complex with estradiol
Components
  • Complex: human rho1 GABAA receptor in complex with estradiol
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit rho-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: N-OCTANE
  • Ligand: DECANE
  • Ligand: DODECANE
  • Ligand: HEXANE
  • Ligand: Pregnenolone sulfate
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: human rho1 GABAA receptor in complex with estradiol

SupramoleculeName: human rho1 GABAA receptor in complex with estradiol / 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: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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 #3: N-OCTANE

MacromoleculeName: N-OCTANE / type: ligand / ID: 3 / Number of copies: 16 / Formula: OCT
Molecular weightTheoretical: 114.229 Da
Chemical component information

ChemComp-OCT:
N-OCTANE

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Macromolecule #4: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 4 / Number of copies: 7 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #5: DODECANE

MacromoleculeName: DODECANE / type: ligand / ID: 5 / Number of copies: 3 / Formula: D12
Molecular weightTheoretical: 170.335 Da
Chemical component information

ChemComp-D12:
DODECANE

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Macromolecule #6: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 6 / Number of copies: 13 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #7: Pregnenolone sulfate

MacromoleculeName: Pregnenolone sulfate / type: ligand / ID: 7 / Number of copies: 1 / Formula: A8W
Molecular weightTheoretical: 396.541 Da
Chemical component information

ChemComp-A8W:
Pregnenolone sulfate / antidepressant*YM

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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: 17 / 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: 42.0 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93154
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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