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- PDB-9jqx: CGP54626-bound-DGABAB -

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Basic information

Entry
Database: PDB / ID: 9jqx
TitleCGP54626-bound-DGABAB
Components
  • Gamma-aminobutyric acid type B receptor subunit 2
  • Metabotropic GABA-B receptor subtype 1
KeywordsMEMBRANE PROTEIN / COMPLEX
Function / homology
Function and homology information


negative regulation of synaptic vesicle fusion to presynaptic active zone membrane / olfactory behavior / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / gamma-aminobutyric acid signaling pathway / cellular response to mechanical stimulus / negative regulation of insulin secretion / G protein-coupled receptor signaling pathway / membrane
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / G-protein coupled receptors family 3 signature 3. / GPCR, family 3, conserved site / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-2BV / Gamma-aminobutyric acid type B receptor subunit 2 / Metabotropic GABA-B receptor subtype 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.61 Å
Authorsshen, C.S. / liu, J.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of GABAB receptor activation during evolution
Authors: shen, C.S. / liu, J.F.
History
DepositionSep 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metabotropic GABA-B receptor subtype 1
B: Gamma-aminobutyric acid type B receptor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,6803
Polymers167,2722
Non-polymers4081
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Metabotropic GABA-B receptor subtype 1


Mass: 79778.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GABA-B-R1, CG15274 / Production host: Homo sapiens (human) / References: UniProt: Q9BML7
#2: Protein Gamma-aminobutyric acid type B receptor subunit 2 / Metabotropic GABA-B receptor subtype 2 / G-protein coupled receptor 51


Mass: 87493.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GABA-B-R2, CG6706 / Production host: Homo sapiens (human) / References: UniProt: Q9BML6
#3: Chemical ChemComp-2BV / (R)-(cyclohexylmethyl)[(2S)-3-{[(1S)-1-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropyl]phosphinic acid / CGP 54626


Mass: 408.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28Cl2NO3P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Drosophila metabotropic GABA-B receptor / Type: COMPLEX / Entity ID: #2, #1 / Source: RECOMBINANT
Molecular weightValue: 200 kDa/nm / Experimental value: YES
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 7 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.0particle selection
12cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36119 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementHighest resolution: 3.61 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00711029
ELECTRON MICROSCOPYf_angle_d0.95314994
ELECTRON MICROSCOPYf_dihedral_angle_d6.6331473
ELECTRON MICROSCOPYf_chiral_restr0.0411702
ELECTRON MICROSCOPYf_plane_restr0.0061879

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