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- PDB-1srz: Solution structure of the second complement control protein (CCP)... -

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Basic information

Entry
Database: PDB / ID: 1srz
TitleSolution structure of the second complement control protein (CCP) module of the GABA(B)R1a receptor, Pro-119 trans conformer
ComponentsGamma-aminobutyric acid type B receptor, subunit 1
KeywordsSIGNALING PROTEIN / GABA(B) receptor / cis-trans isomerization / CCP module / sushi domain / short consensus repeat
Function / homology
Function and homology information


GABA B receptor activation / G protein-coupled receptor dimeric complex / Class C/3 (Metabotropic glutamate/pheromone receptors) / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / 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 / chemical synaptic transmission, postsynaptic / G protein-coupled GABA receptor activity ...GABA B receptor activation / G protein-coupled receptor dimeric complex / Class C/3 (Metabotropic glutamate/pheromone receptors) / G protein-coupled neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential / 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 / chemical synaptic transmission, postsynaptic / 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 / GABA receptor complex / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / synaptic transmission, GABAergic / positive regulation of glutamate secretion / gamma-aminobutyric acid signaling pathway / regulation of glutamate secretion / negative regulation of synaptic transmission / G alpha (i) signalling events / axolemma / GABA-ergic synapse / regulation of postsynaptic membrane potential / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / dendritic shaft / synaptic membrane / mitochondrial membrane / response to nicotine / Schaffer collateral - CA1 synapse / osteoblast differentiation / synaptic vesicle / presynapse / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / perikaryon / response to ethanol / dendritic spine / G protein-coupled receptor signaling pathway / protein heterodimerization activity / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / extracellular space / membrane / plasma membrane / cytoplasm
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / Complement Module, domain 1 / Complement Module; domain 1 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain ...GPCR family 3, gamma-aminobutyric acid receptor, type B1 / GPCR family 3, GABA-B receptor / Complement Module, domain 1 / Complement Module; domain 1 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Ribbon / Mainly Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid type B receptor subunit 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsBlein, S. / Uhrin, D. / Smith, B.O. / White, J.H. / Barlow, P.N.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Analysis of the Complement Control Protein (CCP) Modules of GABAB Receptor 1a: ONLY ONE OF THE TWO CCP MODULES IS COMPACTLY FOLDED
Authors: Blein, S. / Ginham, R. / Uhrin, D. / Smith, B.O. / Soares, D.C. / Veltel, S. / McIlhinney, R.A. / White, J.H. / Barlow, P.N.
History
DepositionMar 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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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)7,4941
Polymers7,4941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 120structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Gamma-aminobutyric acid type B receptor, subunit 1 / GABA-B receptor 1 / GABA-B-R1 / Gb1


Mass: 7494.419 Da / Num. of mol.: 1 / Fragment: Residues 96-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GABBR1 / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: Q9Z0U4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA

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Sample preparation

DetailsContents: 1 mM GABA(B)R1a 2nd CCP module U-15N,13C, 20 mM deuterated sodium acetate buffer, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 4 / Pressure: ambient / Temperature: 310 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionClassification
VNMR6.1collection
Azara2.6processing
ANSIG3.3data analysis
CNS1structure solution
CNS1refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: 1363 unique restraints, 20 dihedral angle restraints (HNHA), 11 hydrogen bonds
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 24

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