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- PDB-6hkc: Solution structure of the Sushi 1 domain of GABAbR1a -

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Basic information

Entry
Database: PDB / ID: 6hkc
TitleSolution structure of the Sushi 1 domain of GABAbR1a
ComponentsGamma-aminobutyric acid type B receptor subunit 1
KeywordsMEMBRANE PROTEIN / neurotransmitter receptor / G protein coupled receptors
Function / homology
Function and homology information


G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / negative regulation of gamma-aminobutyric acid secretion / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion ...G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / GABA B receptor activation / G protein-coupled neurotransmitter receptor activity involved in regulation of presynaptic membrane potential / G protein-coupled GABA receptor complex / negative regulation of gamma-aminobutyric acid secretion / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / negative regulation of epinephrine secretion / negative regulation of dopamine secretion / positive regulation of growth hormone secretion / extracellular matrix protein binding / Class C/3 (Metabotropic glutamate/pheromone receptors) / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / positive regulation of glutamate secretion / negative regulation of synaptic transmission / axolemma / GABA-ergic synapse / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / response to nicotine / mitochondrial membrane / Schaffer collateral - CA1 synapse / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / osteoblast differentiation / synaptic vesicle / presynaptic membrane / G alpha (i) signalling events / postsynaptic membrane / response to ethanol / dendritic spine / protein heterodimerization activity / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / extracellular space / plasma membrane
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. ...GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile. / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Gamma-aminobutyric acid type B receptor subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsVolkov, A.N. / Buts, L. / Van Molle, I.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - FlandersOdyssey Belgium
European Research Council311083 Belgium
CitationJournal: Science / Year: 2019
Title: Secreted amyloid-beta precursor protein functions as a GABABR1a ligand to modulate synaptic transmission.
Authors: Rice, H.C. / de Malmazet, D. / Schreurs, A. / Frere, S. / Van Molle, I. / Volkov, A.N. / Creemers, E. / Vertkin, I. / Nys, J. / Ranaivoson, F.M. / Comoletti, D. / Savas, J.N. / Remaut, H. / ...Authors: Rice, H.C. / de Malmazet, D. / Schreurs, A. / Frere, S. / Van Molle, I. / Volkov, A.N. / Creemers, E. / Vertkin, I. / Nys, J. / Ranaivoson, F.M. / Comoletti, D. / Savas, J.N. / Remaut, H. / Balschun, D. / Wierda, K.D. / Slutsky, I. / Farrow, K. / De Strooper, B. / de Wit, J.
History
DepositionSep 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyric acid type B receptor subunit 1


Theoretical massNumber of molelcules
Total (without water)8,5201
Polymers8,5201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5930 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Gamma-aminobutyric acid type B receptor subunit 1 / Gb1


Mass: 8519.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR1, GPRC3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBS5

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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
121isotropic13D HN(CA)CB
131isotropic13D HN(COCA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HBHA(CO)NH
191isotropic13D C(CO)NH
181isotropic13D (H)CCH-TOCSY
171isotropic12D 1H-13C HSQC
1101isotropic12D 1H-13C HSQC aromatic
1111isotropic13D 1H-15N NOESY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1141isotropic12D (HB)CB(CGCD)HD
1151isotropic12D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] sushi 1, 3 mM APP 9mer, 50 mM potassium phosphate, 50 mM sodium chloride, 0.01 % sodium azide, 90% H2O/10% D2O
Label: sample 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMsushi 1[U-100% 13C; U-100% 15N]1
3 mMAPP 9mernatural abundance1
50 mMpotassium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
0.01 %sodium azidenatural abundance1
Sample conditionsIonic strength: 100 mM / Label: condition 1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CcpNmr AnalysisCCPNpeak picking
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 8
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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