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- EMDB-8922: Cryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamm... -

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Basic information

Entry
Database: EMDB / ID: 8922
TitleCryo-EM structure of the benzodiazepine-sensitive alpha1beta1gamma2S tri-heteromeric GABAA receptor in complex with GABA (Whole map)
Map dataBenzodiazepine-sensitive alpha1-beta1-gamma2 heterotrimeric GABAA receptor in complex with GABA
SampleTriheteromeric alpha1-beta1-gamma2 GABAA receptor
  • (Gamma-aminobutyric acid receptor subunit ...) x 3
  • (ligand) x 4
Function / homologyGamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric-acid A receptor, gamma subunit / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric-acid A receptor, alpha subunit / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel, conserved site ...Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric-acid A receptor, gamma subunit / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric-acid A receptor, alpha subunit / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel transmembrane region / GABA A receptor activation / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel ligand binding domain / anion channel activity / inhibitory extracellular ligand-gated ion channel activity / benzodiazepine receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / GABA-A receptor activity / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / GABA receptor complex / cellular response to histamine / synaptic transmission, GABAergic / inhibitory synapse / gamma-aminobutyric acid signaling pathway / GABA receptor binding / chloride transport / chloride channel activity / chloride channel complex / central nervous system neuron development / dendrite membrane / ligand-gated ion channel activity / ovulation cycle / response to progesterone / ion transport / response to toxic substance / cytoplasmic vesicle membrane / nuclear envelope / postsynaptic membrane / receptor complex / drug binding / cell junction / dendrite / integral component of plasma membrane / membrane / plasma membrane / nucleus / cytoplasm / Gamma-aminobutyric acid receptor subunit beta-1 / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit alpha-1
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsPhulera S / Zhu H / Yu J / Yoshioka C / Gouaux E
CitationJournal: Elife / Year: 2018
Title: Cryo-EM structure of the benzodiazepine-sensitive α1β1γ2S tri-heteromeric GABA receptor in complex with GABA.
Authors: Swastik Phulera / Hongtao Zhu / Jie Yu / Derek P Claxton / Nate Yoder / Craig Yoshioka / Eric Gouaux
Abstract: Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABA ...Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABA receptors are heteromeric assemblies sensitive to many important drugs, from sedatives to anesthetics and anticonvulsant agents, with mutant forms of GABA receptors implicated in multiple neurological diseases. Despite the profound importance of heteromeric GABA receptors in neuroscience and medicine, they have proven recalcitrant to structure determination. Here we present the structure of a tri-heteromeric α1β1γ2S GABA receptor in complex with GABA, determined by single particle cryo-EM at 3.1-3.8 Å resolution, elucidating molecular principles of receptor assembly and agonist binding. Remarkable N-linked glycosylation on the α1 subunit occludes the extracellular vestibule of the ion channel and is poised to modulate receptor assembly and perhaps ion channel gating. Our work provides a pathway to structural studies of heteromeric GABA receptors and a framework for rational design of novel therapeutic agents.
Validation ReportPDB-ID: 6dw0

SummaryFull reportAbout validation report
DateDeposition: Jun 26, 2018 / Header (metadata) release: Aug 1, 2018 / Map release: Aug 8, 2018 / Last update: Aug 8, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 17
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6dw0
  • Surface level: 17
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6dw0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8922.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.3 Å/pix.
= 311.52 Å
240 pix
1.3 Å/pix.
= 311.52 Å
240 pix
1.3 Å/pix.
= 311.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.298 Å
Density
Contour Level:17.0 (by author), 17 (movie #1):
Minimum - Maximum-158.255140000000011 - 137.25609
Average (Standard dev.)-0.073348075 (2.9318972)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.0.0.
Limit239.239.239.
Spacing240240240
CellA=B=C: 311.52 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2981.2981.298
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z311.520311.520311.520
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-158.255137.256-0.073

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Supplemental data

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Sample components

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Entire Triheteromeric alpha1-beta1-gamma2 GABAA receptor

EntireName: Triheteromeric alpha1-beta1-gamma2 GABAA receptor / Details: In complex with alpha1 specific Fab / Number of components: 8

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Component #1: protein, Triheteromeric alpha1-beta1-gamma2 GABAA receptor

ProteinName: Triheteromeric alpha1-beta1-gamma2 GABAA receptor / Details: In complex with alpha1 specific Fab / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: TSA201

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Component #2: protein, Gamma-aminobutyric acid receptor subunit gamma-2

ProteinName: Gamma-aminobutyric acid receptor subunit gamma-2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 56.894949 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-a...

ProteinName: Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 46.267105 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Gamma-aminobutyric acid receptor subunit beta-1,Gamma-am...

ProteinName: Gamma-aminobutyric acid receptor subunit beta-1,Gamma-aminobutyric acid receptor subunit beta-1
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 44.333012 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #6: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #7: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #8: ligand, GAMMA-AMINO-BUTANOIC ACID

LigandName: GAMMA-AMINO-BUTANOIC ACID / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.10312 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.15 mg/ml / pH: 7.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 37 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 120000. X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1200.0 - -2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON III (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1391

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 49417
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: 0.74 / Refinement space: REAL
Output model

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