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Open data
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Basic information
Entry | Database: PDB / ID: 8hc0 | ||||||
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Title | Crystal structure of the extracellular domains of GPR110 | ||||||
![]() | (Adhesion G-protein coupled receptor ...) x 3 | ||||||
![]() | CELL ADHESION / Adhesion GPCR / GPR110 / synaptamide / molecular dynamics simulations | ||||||
Function / homology | ![]() energy reserve metabolic process / fat cell differentiation / regulation of lipid metabolic process / synapse assembly / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / memory / neuron projection development / cytoplasmic vesicle / cell surface receptor signaling pathway ...energy reserve metabolic process / fat cell differentiation / regulation of lipid metabolic process / synapse assembly / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / memory / neuron projection development / cytoplasmic vesicle / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, F.F. / Song, G.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of the Extracellular Domains of GPR110. Authors: Wang, F. / Wang, Y. / Qiu, W. / Zhang, Q. / Yang, H. / Song, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190 KB | Display | ![]() |
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PDB format | ![]() | 149.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 19.8 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Adhesion G-protein coupled receptor ... , 3 types, 3 molecules ACB
#1: Protein | Mass: 39499.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: Q5T601 |
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#2: Protein/peptide | Mass: 2413.712 Da / Num. of mol.: 1 / Fragment: C-terminal Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: Q5T601 |
#3: Protein | Mass: 6612.419 Da / Num. of mol.: 1 / Fragment: N-terminal Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: Q5T601 |
-Sugars , 2 types, 8 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 45 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% PEG-MME 2,000, 15% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→43.8 Å / Num. obs: 18390 / % possible obs: 98 % / Redundancy: 3.18 % / CC1/2: 0.989 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.149 / Net I/σ(I): 9.68 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: predicted by AlphaFold2 Resolution: 2.9→19.8 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 30.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→19.8 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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