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Yorodumi- PDB-7yxa: XFEL crystal structure of the human sphingosine 1 phosphate recep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yxa | |||||||||||||||
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Title | XFEL crystal structure of the human sphingosine 1 phosphate receptor 5 in complex with ONO-5430608 | |||||||||||||||
Components | Sphingosine 1-phosphate receptor 5,Soluble cytochrome b562 | |||||||||||||||
Keywords | MEMBRANE PROTEIN / GPCR / g-protein coupled receptor / XFEL / X-ray free electron laser / serial femtosecond crystallography / SFX / sphingosine-1-phosphate / sphingosine-1-phosphate receptor / S1P5 | |||||||||||||||
Function / homology | Function and homology information sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / regulation of metabolic process / regulation of neuron differentiation / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / membrane => GO:0016020 / periplasmic space ...sphingosine-1-phosphate receptor activity / Lysosphingolipid and LPA receptors / regulation of metabolic process / regulation of neuron differentiation / G protein-coupled receptor activity / electron transport chain / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / membrane => GO:0016020 / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||||||||
Authors | Lyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. ...Lyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. / Khorn, P. / Shevtsov, M. / Kovalev, K. / Okhrimenko, I. / Bukhdruker, S. / Popov, P. / Hu, H. / Weierstall, U. / Liu, W. / Cho, Y. / Gushchin, I. / Rogachev, A. / Bourenkov, G. / Park, S. / Park, G. / Huyn, H.J. / Park, J. / Gordeliy, V. / Borshchevskiy, V. / Mishin, A. / Cherezov, V. | |||||||||||||||
Funding support | Russian Federation, Korea, Republic Of, 4items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis for receptor selectivity and inverse agonism in S1P 5 receptors. Authors: Lyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. / Khorn, P. / Shevtsov, M. / Kovalev, K. / ...Authors: Lyapina, E. / Marin, E. / Gusach, A. / Orekhov, P. / Gerasimov, A. / Luginina, A. / Vakhrameev, D. / Ergasheva, M. / Kovaleva, M. / Khusainov, G. / Khorn, P. / Shevtsov, M. / Kovalev, K. / Bukhdruker, S. / Okhrimenko, I. / Popov, P. / Hu, H. / Weierstall, U. / Liu, W. / Cho, Y. / Gushchin, I. / Rogachev, A. / Bourenkov, G. / Park, S. / Park, G. / Hyun, H.J. / Park, J. / Gordeliy, V. / Borshchevskiy, V. / Mishin, A. / Cherezov, V. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yxa.cif.gz | 433.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yxa.ent.gz | 357.2 KB | Display | PDB format |
PDBx/mmJSON format | 7yxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/7yxa ftp://data.pdbj.org/pub/pdb/validation_reports/yx/7yxa | HTTPS FTP |
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-Related structure data
Related structure data | 3v2yS 4eiyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.11577/1881337 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 49922.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: S1PR5, EDG8, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H228, UniProt: P0ABE7 #2: Sugar | |
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-Non-polymers , 4 types, 201 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.28 Å3/Da / Density % sol: 62.48 % / Description: crystal size less than 10 um |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase / pH: 7 Details: crystallization in syringes in precipitant conditions containing 100-300 mM KH2PO4 monobasic, 28-32% v/v PEG400, and 100 mM HEPES pH 7 Temp details: 20-23 Celcius |
-Data collection
Diffraction | Mean temperature: 296 K / Ambient temp details: helium chamber, 1 atm / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.278 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 7, 2019 / Frequency: 30 |
Radiation | Monochromator: pair of Kirkpatrick-Baez mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.278 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 60071 / % possible obs: 99.93 % / Redundancy: 119.3 % / Biso Wilson estimate: 30.21 Å2 / CC1/2: 0.92 / CC star: 0.979 / R split: 0.244 / Net I/σ(I): 3.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 112 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5883 / CC1/2: 0.154 / CC star: 0.516 / R split: 0.718 / % possible all: 100 |
Serial crystallography measurement | Focal spot size: 6 µm2 / Pulse duration: 25 fsec. / Pulse photon energy: 9700 keV / XFEL pulse repetition rate: 30 Hz |
Serial crystallography sample delivery | Description: LCP injector / Method: injection |
Serial crystallography sample delivery injection | Description: LCP injector / Flow rate: 0.15 µL/min / Injector diameter: 50 µm / Injector temperature: 296 K |
Serial crystallography data reduction | Crystal hits: 6918 / Frames indexed: 6918 / Frames total: 490000 / Lattices indexed: 7492 / XFEL pulse events: 490000 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3v2y, 4eiy Resolution: 2.2→29.97 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.92 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.33 Å2 / Biso mean: 48.9206 Å2 / Biso min: 3.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→29.97 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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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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