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Yorodumi- PDB-6w25: Crystal structure of the Melanocortin-4 Receptor (MC4R) in comple... -
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-Basic information
Entry | Database: PDB / ID: 6w25 | |||||||||
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Title | Crystal structure of the Melanocortin-4 Receptor (MC4R) in complex with SHU9119 | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Melanocortin-4 Receptor / Ca++ cofactor / SHU9119 / GPCR / PGS fusion / LCP | |||||||||
Function / homology | Function and homology information regulation of eating behavior / melanocyte-stimulating hormone receptor activity / response to melanocyte-stimulating hormone / melanocortin receptor activity / glycogen (starch) synthase activity / regulation of grooming behavior / energy reserve metabolic process / regulation of metabolic process / neuropeptide binding / feeding behavior ...regulation of eating behavior / melanocyte-stimulating hormone receptor activity / response to melanocyte-stimulating hormone / melanocortin receptor activity / glycogen (starch) synthase activity / regulation of grooming behavior / energy reserve metabolic process / regulation of metabolic process / neuropeptide binding / feeding behavior / insulin secretion / diet induced thermogenesis / negative regulation of feeding behavior / peptide hormone binding / positive regulation of bone resorption / Peptide ligand-binding receptors / response to insulin / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / nucleotide binding / ubiquitin protein ligase binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Pyrococcus abyssi (archaea) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å | |||||||||
Authors | Yu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. ...Yu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. / Wu, L. / Stevens, S.N. / Peisley, A. / Williams, S.Y. / Chen, V. / Millhauser, G.L. / Zhao, S. / Cone, R.D. / Stevens, R.C. | |||||||||
Citation | Journal: Science / Year: 2020 Title: Determination of the melanocortin-4 receptor structure identifies Ca2+as a cofactor for ligand binding. Authors: Yu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. / Wu, L. / Stevens, S.N. / Peisley, A. / Williams, S.Y. / ...Authors: Yu, J. / Gimenez, L.E. / Hernandez, C.C. / Wu, Y. / Wein, A.H. / Han, G.W. / McClary, K. / Mittal, S.R. / Burdsall, K. / Stauch, B. / Wu, L. / Stevens, S.N. / Peisley, A. / Williams, S.Y. / Chen, V. / Millhauser, G.L. / Zhao, S. / Cone, R.D. / Stevens, R.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w25.cif.gz | 207.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w25.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 6w25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/6w25 ftp://data.pdbj.org/pub/pdb/validation_reports/w2/6w25 | HTTPS FTP |
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-Related structure data
Related structure data | 3emlS S: Starting model for refinement |
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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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Details | authors state that the biological unit is unknown |
-Components
#1: Protein | Mass: 60197.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Pyrococcus abyssi (archaea) Gene: MC4R, PAB2292 / Strain: GE5 / Orsay / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32245, UniProt: Q9V2J8 | ||||
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#2: Protein/peptide | Mass: 1078.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | ChemComp-OLA / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.65 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.9 Details: 19% PEG 400, 100 mM Bis-tris propane buffer, and 50 mM CaCl2 2H2O |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→43.65 Å / Num. obs: 16761 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.997 / Rmerge(I) obs: 0.234 / Net I/σ(I): 11.62 |
Reflection shell | Resolution: 2.75→2.8 Å / Rmerge(I) obs: 3.302 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 847 / CC1/2: 0.561 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 3EML Resolution: 2.75→43.65 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.878 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.027 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.916 / SU Rfree Blow DPI: 0.33 / SU Rfree Cruickshank DPI: 0.339
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Displacement parameters | Biso max: 186.18 Å2 / Biso mean: 79.91 Å2 / Biso min: 45.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.75→43.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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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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