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- PDB-4ms3: Crystal structure of the extracellular domain of human GABA(B) re... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ms3 | |||||||||
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Title | Crystal structure of the extracellular domain of human GABA(B) receptor bound to the endogenous agonist GABA | |||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Geng, Y. / Bush, M. / Mosyak, L. / Wang, F. / Fan, Q.R. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.7 KB | Display | ![]() |
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PDB format | ![]() | 140.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4mqeSC ![]() 4mqfC ![]() 4mr7C ![]() 4mr8C ![]() 4mr9C ![]() 4mrmC ![]() 4ms1C ![]() 4ms4C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#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.) ![]() ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-ABU / ![]() |
#4: Sugar | ChemComp-NAG / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Sequence details | SUBUNIT 1 IS RESIDUES 48-459 OF ISOFORM 1B (UNP Q9UBS5-2). |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 18% PEG2000, 5% glycerol, 0.15 M ammonium chloride, 0.1 M sodium cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→60.388 Å / Num. all: 33921 / Num. obs: 33921 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 50.45 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 11.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4MQE Resolution: 2.5→33.65 Å / Cor.coef. Fo:Fc: 0.9065 / Cor.coef. Fo:Fc free: 0.8963 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.517 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / SU R Blow DPI: 0.567 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.259 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 126.27 Å2 / Biso mean: 42.7166 Å2 / Biso min: 7.37 Å2
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Refine analyze | Luzzati coordinate error obs: 0.317 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→33.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.58 Å / Total num. of bins used: 17
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