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- PDB-6me6: XFEL crystal structure of human melatonin receptor MT2 in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6me6 | ||||||
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Title | XFEL crystal structure of human melatonin receptor MT2 in complex with 2-phenylmelatonin | ||||||
![]() | Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin | ||||||
![]() | MEMBRANE PROTEIN / GPCR / melatonin receptor type 1B (MT2) / 2-phenylmelatonin / XFEL / LCP / BRIL / Rubredoxin / circadian rhythm / jetlag / type 2 diabetes | ||||||
Function / homology | ![]() positive regulation of circadian sleep/wake cycle, non-REM sleep / melatonin receptor activity / regulation of neuronal action potential / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / alkane catabolic process / Class A/1 (Rhodopsin-like receptors) / camera-type eye development / negative regulation of vasoconstriction / negative regulation of cGMP-mediated signaling ...positive regulation of circadian sleep/wake cycle, non-REM sleep / melatonin receptor activity / regulation of neuronal action potential / negative regulation of transmission of nerve impulse / positive regulation of transmission of nerve impulse / alkane catabolic process / Class A/1 (Rhodopsin-like receptors) / camera-type eye development / negative regulation of vasoconstriction / negative regulation of cGMP-mediated signaling / negative regulation of cytosolic calcium ion concentration / regulation of insulin secretion / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of insulin secretion / G protein-coupled receptor activity / electron transport chain / glucose homeostasis / G alpha (i) signalling events / chemical synaptic transmission / negative regulation of neuron apoptotic process / periplasmic space / electron transfer activity / iron ion binding / G protein-coupled receptor signaling pathway / synapse / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johansson, L.C. / Stauch, B. / McCorvy, J. / Han, G.W. / Patel, N. / Batyuk, A. / Gati, C. / Li, C. / Grandner, J. / Hao, S. ...Johansson, L.C. / Stauch, B. / McCorvy, J. / Han, G.W. / Patel, N. / Batyuk, A. / Gati, C. / Li, C. / Grandner, J. / Hao, S. / Olsen, R.H.J. / Tribo, A.R. / Zaare, S. / Zhu, L. / Zatsepin, N.A. / Weierstall, U. / Liu, W. / Roth, B.L. / Katritch, V. / Cherezov, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: XFEL structures of the human MT2melatonin receptor reveal the basis of subtype selectivity. Authors: Johansson, L.C. / Stauch, B. / McCorvy, J.D. / Han, G.W. / Patel, N. / Huang, X.P. / Batyuk, A. / Gati, C. / Slocum, S.T. / Li, C. / Grandner, J.M. / Hao, S. / Olsen, R.H.J. / Tribo, A.R. / ...Authors: Johansson, L.C. / Stauch, B. / McCorvy, J.D. / Han, G.W. / Patel, N. / Huang, X.P. / Batyuk, A. / Gati, C. / Slocum, S.T. / Li, C. / Grandner, J.M. / Hao, S. / Olsen, R.H.J. / Tribo, A.R. / Zaare, S. / Zhu, L. / Zatsepin, N.A. / Weierstall, U. / Yous, S. / Stevens, R.C. / Liu, W. / Roth, B.L. / Katritch, V. / 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 | ![]() | 175.4 KB | Display | ![]() |
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PDB format | ![]() | 133.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6me7C ![]() 6me8C ![]() 6me9C ![]() 1iroS 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 | BIOLOGICAL UNIT IS UNKNOWN |
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Components
#1: Protein | Mass: 51514.578 Da / Num. of mol.: 2 Mutation: M2007W, H2102I, R2106L, P37S, D86N, L108F, F129W, N137D, C140L, W246F, A305P Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Gene: cybC, MTNR1B / Production host: ![]() ![]() References: UniProt: P0ABE7, UniProt: P49286, UniProt: P00268 #2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-OLC / ( | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.25 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: N-(2-Acetamido)iminodiacetic acid, PEG 400, ammonium acetate |
-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: Aug 20, 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: 2.8→21.99 Å / Num. obs: 35706 / % possible obs: 100 % / Redundancy: 571.2 % / Biso Wilson estimate: 88.06 Å2 / Net I/σ(I): 0.14 |
Reflection shell | Resolution: 2.8→2.88 Å / Redundancy: 141.3 % / Num. unique obs: 2887 / R split: 4.307 / % possible all: 100 |
Serial crystallography measurement | Pulse duration: 43 fsec. / Pulse energy: 4 µJ / Pulse photon energy: 9.52 keV / XFEL pulse repetition rate: 120 Hz |
Serial crystallography sample delivery | Method: injection |
Serial crystallography sample delivery injection | Carrier solvent: LCP / Flow rate: 0.3 µL/min / Injector diameter: 50 µm / Injector nozzle: LCP / Power by: HPLC pump |
Serial crystallography data reduction | Crystal hits: 84928 / Frames indexed: 31677 / Frames total: 2154963 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB id: 1IRO Resolution: 2.8→21.99 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.898 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.423 / SU Rfree Blow DPI: 0.279 / SU Rfree Cruickshank DPI: 0.293
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Displacement parameters | Biso mean: 130.54 Å2
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Refine analyze | Luzzati coordinate error obs: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→21.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
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