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- EMDB-21533: CryoEM Structure of Inactive GABAB Heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-21533
TitleCryoEM Structure of Inactive GABAB Heterodimer
Map data
SampleGABAB Heterodimer
  • (Gamma-aminobutyric acid type B receptor subunit ...) x 2
  • (ligand) x 4
Function / homology
Function and homology information


G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / neuron-glial cell signaling / G protein-coupled receptor heterodimeric complex / G protein-coupled GABA receptor activity / GABA receptor complex / negative regulation of adenylate cyclase activity / gamma-aminobutyric acid signaling pathway / GABA-ergic synapse / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Schaffer collateral - CA1 synapse ...G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / neuron-glial cell signaling / G protein-coupled receptor heterodimeric complex / G protein-coupled GABA receptor activity / GABA receptor complex / negative regulation of adenylate cyclase activity / gamma-aminobutyric acid signaling pathway / GABA-ergic synapse / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Schaffer collateral - CA1 synapse / presynaptic membrane / transmembrane signaling receptor activity / postsynaptic membrane / chemical synaptic transmission / protein heterodimerization activity / neuron projection / G protein-coupled receptor signaling pathway / dendrite / integral component of plasma membrane / extracellular region / plasma membrane / cytoplasm
GPCR family 3, gamma-aminobutyric acid receptor, type B2 / GPCR family 3, GABA-B receptor / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Sushi/SCR/CCP superfamily / Periplasmic binding protein-like I / GPCR, family 3, conserved site / GPCR family 3, C-terminal / GPCR, family 3 / Sushi/SCR/CCP domain / Receptor, ligand binding region
Gamma-aminobutyric acid type B receptor subunit 2 / Gamma-aminobutyric acid type B receptor subunit 1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsPapasergi-Scott MM / Robertson MJ / Skiniotis G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R01NS092695-01 United States
CitationJournal: Nature / Year: 2020
Title: Structures of metabotropic GABA receptor.
Authors: Makaía M Papasergi-Scott / Michael J Robertson / Alpay B Seven / Ouliana Panova / Jesper M Mathiesen / Georgios Skiniotis /
Abstract: GABA (γ-aminobutyric acid) stimulation of the metabotropic GABA receptor results in prolonged inhibition of neurotransmission that is central to brain physiology. GABA belongs to the Family C of G ...GABA (γ-aminobutyric acid) stimulation of the metabotropic GABA receptor results in prolonged inhibition of neurotransmission that is central to brain physiology. GABA belongs to the Family C of G protein-coupled receptors (GPCRs), which operate as dimers to relay synaptic neurotransmitter signals into a cellular response through the binding and activation of heterotrimeric G proteins. GABA, however, is unique in its function as an obligate heterodimer in which agonist binding and G protein activation take place on distinct subunits. Here we show structures of heterodimeric and homodimeric full-length GABA receptors. Complemented by cellular signaling assays and atomistic simulations, the structures reveal an essential role for the GABA extracellular loop 2 (ECL2) in relaying structural transitions by ordering the linker connecting the extracellular ligand-binding domain to the transmembrane region. Furthermore, the ECL2 of both GABA subunits caps and interacts with the hydrophilic head of a phospholipid occupying the extracellular half of the transmembrane domain, thereby providing a potentially crucial link between ligand binding and the receptor core that engages G protein. These results provide a starting framework to decipher mechanistic modes of signal transduction mediated by GABA dimers and have important implications for rational drug design targeting these receptors.
Validation ReportPDB-ID: 6w2x

SummaryFull reportAbout validation report
History
DepositionMar 8, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6w2x
  • Surface level: 0.0168
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_21533.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 380 pix.
= 323.798 Å
0.85 Å/pix.
x 380 pix.
= 323.798 Å
0.85 Å/pix.
x 380 pix.
= 323.798 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8521 Å
Density
Contour LevelBy AUTHOR: 0.0168 / Movie #1: 0.0168
Minimum - Maximum-0.14691305 - 0.17749089
Average (Standard dev.)0.0000944169 (±0.0022107814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 323.798 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85210.85210.8521
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z323.798323.798323.798
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.1470.1770.000

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Supplemental data

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Additional map: Inactive state heterodimer of GABAB focused refinement on...

Fileemd_21533_additional.map
AnnotationInactive state heterodimer of GABAB focused refinement on VFT and linker region.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire GABAB Heterodimer

EntireName: GABAB Heterodimer / Number of components: 7

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Component #1: protein, GABAB Heterodimer

ProteinName: GABAB Heterodimer / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #2: protein, Gamma-aminobutyric acid type B receptor subunit 1

ProteinName: Gamma-aminobutyric acid type B receptor subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 94.17357 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, Gamma-aminobutyric acid type B receptor subunit 2

ProteinName: Gamma-aminobutyric acid type B receptor subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 102.799164 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(...

LigandName: (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.74605 kDa

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Component #6: ligand, [(2~{S})-3-[[(1~{S})-1-(3,4-dichlorophenyl)ethyl]amino]-2...

LigandName: [(2~{S})-3-[[(1~{S})-1-(3,4-dichlorophenyl)ethyl]amino]-2-oxidanyl-propyl]-(phenylmethyl)phosphinic acid
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.402252 kDa

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Component #7: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 291 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60.5 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 286140
3D reconstructionSoftware: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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