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- PDB-6me5: XFEL crystal structure of human melatonin receptor MT1 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6me5 | ||||||
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Title | XFEL crystal structure of human melatonin receptor MT1 in complex with agomelatine | ||||||
![]() | chimera protein of Melatonin receptor type 1A and GlgA glycogen synthase | ||||||
![]() | MEMBRANE PROTEIN / GPCR / melatonin receptor type 1A (MT1) / agomelatine / XFEL / LCP / PGS / circadian rhythm / jetlag | ||||||
Function / homology | ![]() melatonin receptor activity / glycogen (starch) synthase activity / organic cyclic compound binding / hormone binding / Class A/1 (Rhodopsin-like receptors) / glycogen biosynthetic process / mating behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity ...melatonin receptor activity / glycogen (starch) synthase activity / organic cyclic compound binding / hormone binding / Class A/1 (Rhodopsin-like receptors) / glycogen biosynthetic process / mating behavior / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / circadian rhythm / G alpha (i) signalling events / receptor complex / G protein-coupled receptor signaling pathway / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Gati, C. / Batyuk, A. / Ishchenko, A. / Brehm, W. / White, T.A. ...Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Gati, C. / Batyuk, A. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, C. / Zhu, L. / Grant, T.D. / Grandner, J.M. / Olsen, R.H.J. / Tribo, A.R. / Weierstall, U. / Roth, B.L. / Katritch, V. / Liu, W. / Cherezov, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of ligand recognition at the human MT1melatonin receptor. Authors: Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Huang, X.P. / Gati, C. / Batyuk, A. / Slocum, S.T. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, ...Authors: Stauch, B. / Johansson, L.C. / McCorvy, J.D. / Patel, N. / Han, G.W. / Huang, X.P. / Gati, C. / Batyuk, A. / Slocum, S.T. / Ishchenko, A. / Brehm, W. / White, T.A. / Michaelian, N. / Madsen, C. / Zhu, L. / Grant, T.D. / Grandner, J.M. / Shiriaeva, A. / Olsen, R.H.J. / Tribo, A.R. / Yous, S. / Stevens, R.C. / Weierstall, U. / Katritch, V. / Roth, B.L. / Liu, W. / Cherezov, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.3 KB | Display | ![]() |
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PDB format | ![]() | 80.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 821.2 KB | Display | ![]() |
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Full document | ![]() | 822.7 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6me2C ![]() 6me3C ![]() 6me4C ![]() 4s0vS 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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Details | AUTHORS STATE BIOLOGICAL UNIT IS UNKNOWN |
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Components
#1: Protein | Mass: 56597.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MTNR1A, PAB2292 / Strain: GE5 / Orsay / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-AWY / ~{ |
#3: Chemical | ChemComp-OLA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.05 Å3/Da / Density % sol: 69.63 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 60-100 mM potassium phosphate monobasic, 32-35% (vol/vol) PEG 400, 100 mM HEPES pH 7.0, 1 mM ligand, 2.5% (vol/vol) DMSO, 1.5% (vol/vol) propan-2-ol |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→28.9 Å / Num. obs: 15917 / % possible obs: 100 % / Redundancy: 15917 % / Biso Wilson estimate: 64.1 Å2 / R split: 0.12 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 3.2→3.42 Å / Redundancy: 151.6 % / Mean I/σ(I) obs: 0.7 / R split: 1.673 / % possible all: 100 |
Serial crystallography measurement | Pulse duration: 30 fsec. / Pulse energy: 3 µJ / Pulse photon energy: 9.83 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: LCP / Flow rate: 0.357 µL/min / Injector diameter: 50 µm / Injector nozzle: LCP / Power by: HPLC |
Serial crystallography data reduction | Crystal hits: 45820 / Frames indexed: 43423 / Frames total: 466602 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4S0V Resolution: 3.2→28.87 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.918 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.375 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 1.445 / SU Rfree Blow DPI: 0.391 / SU Rfree Cruickshank DPI: 0.396
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Displacement parameters | Biso mean: 114.65 Å2
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Refine analyze | Luzzati coordinate error obs: 0.58 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.2→28.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.42 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
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