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Yorodumi- PDB-4mr7: Crystal structure of the extracellular domain of human GABA(B) re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mr7 | |||||||||
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Title | Crystal structure of the extracellular domain of human GABA(B) receptor bound to the antagonist CGP54626 | |||||||||
Components | (Gamma-aminobutyric acid type B receptor subunit ...) x 2 | |||||||||
Keywords | SIGNALING PROTEIN/ANTAGONIST / heterodimeric protein complex / Venus Flytrap module / neurotransmitter receptor / SIGNALING PROTEIN-ANTAGONIST complex | |||||||||
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) / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / 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 / Schaffer collateral - CA1 synapse / mitochondrial membrane / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / transmembrane signaling receptor activity / osteoblast differentiation / synaptic vesicle / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / neuron projection / protein heterodimerization activity / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / neuronal cell body / glutamatergic synapse / endoplasmic reticulum membrane / extracellular space / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||
Authors | Geng, Y. / Bush, M. / Mosyak, L. / Wang, F. / Fan, Q.R. | |||||||||
Citation | Journal: Nature / Year: 2013 Title: Structural mechanism of ligand activation in human GABA(B) receptor. Authors: Geng, Y. / Bush, M. / Mosyak, L. / Wang, F. / Fan, Q.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mr7.cif.gz | 195.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mr7.ent.gz | 150 KB | Display | PDB format |
PDBx/mmJSON format | 4mr7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mr7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4mr7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4mr7_validation.xml.gz | 36.1 KB | Display | |
Data in CIF | 4mr7_validation.cif.gz | 53.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/4mr7 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/4mr7 | HTTPS FTP |
-Related structure data
Related structure data | 4mqeSC 4mqfC 4mr8C 4mr9C 4mrmC 4ms1C 4ms3C 4ms4C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Gamma-aminobutyric acid type B receptor subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 47645.648 Da / Num. of mol.: 1 / Fragment: extracellular domain (SEE REMARK 999) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR1, GPRC3A / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: Q9UBS5 |
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#2: Protein | Mass: 49127.492 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 42-466) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABBR2, GPR51, GPRC3B / Plasmid: pFBDM / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: O75899 |
-Sugars , 3 types, 3 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 505 molecules
#5: Chemical | ChemComp-2BV / ( |
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#7: Water | ChemComp-HOH / |
-Details
Sequence details | SUBUNIT 1 IS RESIDUES 48-459 OF ISOFORM 1B (UNP Q9UBS5-2). |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG3350, 20% glycerol, 0.12 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→100 Å / Num. all: 57756 / Num. obs: 57756 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 30.23 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Χ2: 1.01 / Net I/σ(I): 14.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4MQE Resolution: 2.15→21.67 Å / Cor.coef. Fo:Fc: 0.9321 / Cor.coef. Fo:Fc free: 0.9034 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / SU R Blow DPI: 0.251 / SU Rfree Blow DPI: 0.198 / SU Rfree Cruickshank DPI: 0.199 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 129.28 Å2 / Biso mean: 39.0369 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.298 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→21.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Total num. of bins used: 20
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