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- EMDB-30301: Cryo-EM structure of the CGP54626-bound human GABA(B) receptor in... -

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Basic information

Entry
Database: EMDB / ID: EMD-30301
TitleCryo-EM structure of the CGP54626-bound human GABA(B) receptor in inactive state.
Map data
SampleThe CGP54626-bound GABAB heterodimer
  • (Gamma-aminobutyric acid type B receptor subunit ...) x 2
  • (ligand) x 2
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: 2.9 Å
AuthorsMao C / Shen C / Li C / Shen D / Xu C / Zhang S / Zhou R / Shen Q / Chen L / Jiang Z / Liu J / Zhang Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81922071 China
Ministry of Science and Technology (MoST, China)2018YFA0507003 China
CitationJournal: Cell Res. / Year: 2020
Title: Cryo-EM structures of inactive and active GABA receptor.
Authors: Chunyou Mao / Cangsong Shen / Chuntao Li / Dan-Dan Shen / Chanjuan Xu / Shenglan Zhang / Rui Zhou / Qingya Shen / Li-Nan Chen / Zhinong Jiang / Jianfeng Liu / Yan Zhang /
Abstract: Metabotropic GABA G protein-coupled receptor functions as a mandatory heterodimer of GB1 and GB2 subunits and mediates inhibitory neurotransmission in the central nervous system. Each subunit is ...Metabotropic GABA G protein-coupled receptor functions as a mandatory heterodimer of GB1 and GB2 subunits and mediates inhibitory neurotransmission in the central nervous system. Each subunit is composed of the extracellular Venus flytrap (VFT) domain and transmembrane (TM) domain. Here we present cryo-EM structures of full-length human heterodimeric GABA receptor in the antagonist-bound inactive state and in the active state complexed with an agonist and a positive allosteric modulator in the presence of G protein at a resolution range of 2.8-3.0 Å. Our structures reveal that agonist binding stabilizes the closure of GB1 VFT, which in turn triggers a rearrangement of TM interfaces between the two subunits from TM3-TM5/TM3-TM5 in the inactive state to TM6/TM6 in the active state and finally induces the opening of intracellular loop 3 and synergistic shifting of TM3, 4 and 5 helices in GB2 TM domain to accommodate the α5-helix of G. We also observed that the positive allosteric modulator anchors at the dimeric interface of TM domains. These results provide a structural framework for understanding class C GPCR activation and a rational template for allosteric modulator design targeting the dimeric interface of GABA receptor.
Validation ReportPDB-ID: 7c7s

SummaryFull reportAbout validation report
History
DepositionMay 26, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateJul 1, 2020-
Current statusJul 1, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7c7s
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30301.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 320 pix.
= 324.48 Å
1.01 Å/pix.
x 320 pix.
= 324.48 Å
1.01 Å/pix.
x 320 pix.
= 324.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.038844854 - 0.33748716
Average (Standard dev.)0.00021128019 (±0.0043344493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 324.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z324.480324.480324.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0390.3370.000

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Supplemental data

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Additional map: The overall refinement map of the CGP54626-bound GABAB heterodimer.

Fileemd_30301_additional.map
AnnotationThe overall refinement map of the CGP54626-bound GABAB heterodimer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire The CGP54626-bound GABAB heterodimer

EntireName: The CGP54626-bound GABAB heterodimer / Number of components: 5

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Component #1: protein, The CGP54626-bound GABAB heterodimer

ProteinName: The CGP54626-bound GABAB heterodimer / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK 293F

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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: 105.976297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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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: 91.359445 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #5: ligand, (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichloropheny...

LigandName: (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.4083 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / 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: 64 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal), 49310 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4740

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 374589
3D reconstructionSoftware: RELION / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Input PDB model: 4MR7
Output model

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