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- PDB-5ws3: Crystal structures of human orexin 2 receptor bound to the select... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ws3 | |||||||||||||||
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Title | Crystal structures of human orexin 2 receptor bound to the selective antagonist EMPA determined by serial femtosecond crystallography at SACLA | |||||||||||||||
![]() | Orexin receptor type 2,GlgA glycogen synthase,Orexin receptor type 2 | |||||||||||||||
![]() | SIGNALING PROTEIN / receptor | |||||||||||||||
Function / homology | ![]() regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuropeptide receptor activity / glycogen (starch) synthase activity / feeding behavior / locomotion / glycogen biosynthetic process / peptide hormone binding ...regulation of circadian sleep/wake cycle, wakefulness / circadian sleep/wake cycle process / orexin receptor activity / Orexin and neuropeptides FF and QRFP bind to their respective receptors / neuropeptide receptor activity / glycogen (starch) synthase activity / feeding behavior / locomotion / glycogen biosynthetic process / peptide hormone binding / neuropeptide signaling pathway / cellular response to hormone stimulus / regulation of cytosolic calcium ion concentration / peptide binding / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / synapse / plasma membrane / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Suno, R. / Kimura, K. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Tsujimoto, H. / Sasanuma, M. ...Suno, R. / Kimura, K. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Tsujimoto, H. / Sasanuma, M. / Horita, S. / Hirokawa, T. / Nango, E. / Tono, K. / Kameshima, T. / Hatsui, T. / Joti, Y. / Yabashi, M. / Shimamoto, K. / Yamamoto, M. / Rosenbaum, D.M. / Iwata, S. / Shimamura, T. / Kobayashi, T. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA. Authors: Suno, R. / Kimura, K.T. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Horita, S. / Tsujimoto, H. / Tawaramoto, M.S. / Hirokawa, T. / Nango, E. / Tono, K. / ...Authors: Suno, R. / Kimura, K.T. / Nakane, T. / Yamashita, K. / Wang, J. / Fujiwara, T. / Yamanaka, Y. / Im, D. / Horita, S. / Tsujimoto, H. / Tawaramoto, M.S. / Hirokawa, T. / Nango, E. / Tono, K. / Kameshima, T. / Hatsui, T. / Joti, Y. / Yabashi, M. / Shimamoto, K. / Yamamoto, M. / Rosenbaum, D.M. / Iwata, S. / Shimamura, T. / Kobayashi, T. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.9 KB | Display | ![]() |
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PDB format | ![]() | 179.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wqcC ![]() 4s0vS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 64204.871 Da / Num. of mol.: 1 Fragment: UNP residues 3-254,UNP residues 218-413,UNP residues 294-388 Source method: isolated from a genetically manipulated source Details: Chimera protein of UNP residues 3-254 from Orexin receptor type 2 (O43614), UNP residues 218-413 from GlgA glycogen synthase (Q9V2J8), UNP residues 294-388 from Orexin receptor type 2 (O43614) Source: (gene. exp.) ![]() ![]() ![]() Gene: HCRTR2, PAB2292 / Strain: GE5 / Orsay / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-7MA / | ||||
#3: Chemical | ChemComp-OLA / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 6 Details: 0.1M MES, 0.1M sodium malonate, 27-30% PEG 300, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MPCCD / Detector: CCD / Date: Apr 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.77 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 28958 / % possible obs: 100 % / Redundancy: 77.6 % / CC1/2: 0.98 / Net I/σ(I): 5.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.2 % / CC1/2: 0.58 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4s0v Resolution: 2.3→45.109 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.5 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.109 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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