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- PDB-4pas: Heterodimeric coiled-coil structure of human GABA(B) receptor -

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Basic information

Entry
Database: PDB / ID: 4pas
TitleHeterodimeric coiled-coil structure of human GABA(B) receptor
Components
  • Gamma-aminobutyric acid type B receptor subunit 1
  • Gamma-aminobutyric acid type B receptor subunit 2
KeywordsSIGNALING PROTEIN / GABA(B) receptor / coiled-coil / heterodimer
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 / GABA receptor complex / negative regulation of adenylate cyclase activity / 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 / transmembrane signaling receptor activity / synaptic vesicle / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / neuron projection / 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 / plasma membrane / cytoplasm
Similarity search - Function
GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / 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 / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR ...GPCR family 3, gamma-aminobutyric acid receptor, type B2 / Gamma-aminobutyric acid type B receptor subunit 2, coiled-coil domain / Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain / 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 / 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 2 / Gamma-aminobutyric acid type B receptor subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.62 Å
AuthorsBurmakina, S. / Geng, Y. / Chen, Y. / Fan, Q.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM088454-05 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Heterodimeric coiled-coil interactions of human GABAB receptor.
Authors: Burmakina, S. / Geng, Y. / Chen, Y. / Fan, Q.R.
History
DepositionApr 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid type B receptor subunit 1
B: Gamma-aminobutyric acid type B receptor subunit 2


Theoretical massNumber of molelcules
Total (without water)9,7362
Polymers9,7362
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-15 kcal/mol
Surface area5810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.721, 54.654, 55.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 5003.499 Da / Num. of mol.: 1 / Fragment: UNP residues 762-802
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR1, GPRC3A / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q9UBS5
#2: Protein/peptide Gamma-aminobutyric acid type B receptor subunit 2 / Gb2 / G-protein coupled receptor 51 / HG20


Mass: 4732.224 Da / Num. of mol.: 1 / Fragment: UNP residues 779-819
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR2, GPR51, GPRC3B / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: O75899
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 3.0M ammonium sulphate, 0.1M bicine, pH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898,0.97934,0.96863
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 11, 2008
RadiationMonochromator: KOHZU double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979341
30.968631
ReflectionResolution: 1.62→50 Å / Num. all: 8951 / Num. obs: 8951 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Χ2: 1.398 / Net I/av σ(I): 50.758 / Net I/σ(I): 43.8 / Num. measured all: 53628
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.62-1.682.90.05517.796941.12176.3
1.68-1.753.40.0588331.20691.1
1.75-1.824.20.059061.27498.3
1.82-1.926.20.0539121.491100
1.92-2.047.20.0469211.391100
2.04-2.27.20.0389361.521100
2.2-2.427.20.0349311.419100
2.42-2.777.20.0349461.368100
2.77-3.4970.0349391.35599.6
3.49-506.30.0359331.45792.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.4.0066refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.62→35.51 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.157 / SU ML: 0.056 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 471 5.3 %RANDOM
Rwork0.1925 8455 --
obs0.1938 8926 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 47.55 Å2 / Biso mean: 14.407 Å2 / Biso min: 2.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.62→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms614 0 0 75 689
Biso mean---25.49 -
Num. residues----74
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021617
X-RAY DIFFRACTIONr_angle_refined_deg0.8271.995821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.178572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31425.83336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90215141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.447156
X-RAY DIFFRACTIONr_chiral_restr0.050.293
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02452
X-RAY DIFFRACTIONr_mcbond_it1.4545369
X-RAY DIFFRACTIONr_mcangle_it2.5636594
X-RAY DIFFRACTIONr_scbond_it3.1046248
X-RAY DIFFRACTIONr_scangle_it5.2317.5227
LS refinement shellResolution: 1.62→1.707 Å
RfactorNum. reflection% reflection
Rfree0.251 57 5.3 %
Rwork0.196 1011 -
obs--80.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.3742-0.3581-1.29730.69211.11324.5456-0.0590.0452-0.06980.017-0.06210.06470.0766-0.0950.12110.0016-0.00310.01110.0096-0.0102-0.0024GBR1b coiled-coil10.27665.666810.9002
20.09020.0412-0.59030.3595-0.99885.4213-0.03840.01750.02630.046-0.0091-0.0379-0.0430.0080.0475-0.00110.0044-0.00830.02060.0041-0.0152GBR2 coiled-coil17.69810.16319.1285
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A767 - 801
2X-RAY DIFFRACTION2B779 - 817

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