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- PDB-5x9x: Solution structure of heterodimeric coiled-coil domain of Drosoph... -

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Basic information

Entry
Database: PDB / ID: 5x9x
TitleSolution structure of heterodimeric coiled-coil domain of Drosophila GABAB receptor 1 and 2
Components
  • Metabotropic GABA-B receptor subtype 1
  • Metabotropic GABA-B receptor subtype 2
KeywordsSIGNALING PROTEIN / GABAB receptor / Drosophila / coiled-coil
Function / homology
Function and homology information


negative regulation of synaptic vesicle fusion to presynaptic active zone membrane / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / olfactory behavior / gamma-aminobutyric acid signaling pathway / negative regulation of insulin secretion / cellular response to mechanical stimulus / membrane => GO:0016020 / G protein-coupled receptor signaling pathway / membrane / plasma membrane
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / GPCR, family 3, conserved site / G-protein coupled receptors family 3 signature 3. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Metabotropic GABA-B receptor subtype 2 / Metabotropic GABA-B receptor subtype 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, X. / Zhang, S. / Liu, J. / Zhang, C.X.
CitationJournal: To Be Published
Title: Solution structure of heterodimeric coiled-coil domain of Drosophila GABAB receptor 1 and 2
Authors: Liu, X. / Zhang, S.
History
DepositionMar 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Metabotropic GABA-B receptor subtype 1
B: Metabotropic GABA-B receptor subtype 2


Theoretical massNumber of molelcules
Total (without water)10,5602
Polymers10,5602
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2030 Å2
ΔGint-21 kcal/mol
Surface area7240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Metabotropic GABA-B receptor subtype 1


Mass: 5412.098 Da / Num. of mol.: 1 / Fragment: Coiled coil domain, UNP residues 755-796
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GABA-B-R1, CG15274 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BML7
#2: Protein/peptide Metabotropic GABA-B receptor subtype 2 / GABAB receptor 2


Mass: 5147.888 Da / Num. of mol.: 1 / Fragment: coiled coil domain, UNP residues 740-780 / Mutation: C102S,C116S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: GABA-B-R2, CG6706 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BML6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
122isotropic12D 1H-15N HSQC
132isotropic12D 1H-13C HSQC aliphatic
142isotropic13D CBCA(CO)NH
152isotropic13D HN(CA)CB
1122isotropic13D HNCO
1112isotropic13D (H)CCH-TOCSY
1102isotropic13D CCH-TOCSY
192isotropic13D 1H-13C NOESY
181isotropic13D 1H-15N NOESY
172isotropic13D HBHA(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution120 mM PBS, 100 mM NaCl, 0.02 mg/mL NaN3, 0.8 mM [U-99% 15N] coiled-coil domain of Drosophila GABAB receptor 1, 0.8 mM [U-99% 15N] coiled-coil domain of Drosophila GABAB receptor 2, 90% H2O/10% D2ON_sample90% H2O/10% D2O
solution220 mM PBS, 100 mM NaCl, 0.02 mg/mL NaN3, 0.7 mM [U-13C; U-15N] coiled-coil domain of Drosophila GABAB receptor 1, 0.7 mM [U-13C; U-15N] coiled-coil domain of Drosophila GABAB receptor 2, 90% H2O/10% D2OCN_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMPBSnatural abundance1
100 mMNaClnatural abundance1
0.02 mg/mLNaN3natural abundance1
0.8 mMcoiled-coil domain of Drosophila GABAB receptor 1[U-99% 15N]1
0.8 mMcoiled-coil domain of Drosophila GABAB receptor 2[U-99% 15N]1
20 mMPBSnatural abundance2
100 mMNaClnatural abundance2
0.02 mg/mLNaN3natural abundance2
0.7 mMcoiled-coil domain of Drosophila GABAB receptor 1[U-13C; U-15N]2
0.7 mMcoiled-coil domain of Drosophila GABAB receptor 2[U-13C; U-15N]2
Sample conditionsIonic strength: 120 mM / Label: 1 / pH: 7.0 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Agilent DD2 600 / Manufacturer: Agilent / Model: DD2 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNMR2.3CCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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