[English] 日本語
Yorodumi- PDB-6me8: XFEL crystal structure of human melatonin receptor MT2 (N86D) in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6me8 | ||||||
---|---|---|---|---|---|---|---|
Title | XFEL crystal structure of human melatonin receptor MT2 (N86D) in complex with 2-phenylmelatonin | ||||||
Components | Soluble cytochrome b562,Melatonin receptor type 1B,Rubredoxin | ||||||
Keywords | MEMBRANE PROTEIN / GPCR / melatonin receptor type 1B (MT2) / N86D mutation / 2-phenylmelatonin / XFEL / LCP / BRIL / Rubredoxin / circadian rhythm / jetlag / type 2 diabetes | ||||||
Function / homology | Function and homology information 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 / heme binding / synapse / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) Clostridium pasteurianum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | 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 | United States, 1items
| ||||||
Citation | Journal: Nature / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6me8.cif.gz | 171.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6me8.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 6me8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6me8_validation.pdf.gz | 937.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6me8_full_validation.pdf.gz | 940.2 KB | Display | |
Data in XML | 6me8_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6me8_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/6me8 ftp://data.pdbj.org/pub/pdb/validation_reports/me/6me8 | HTTPS FTP |
-Related structure data
Related structure data | 6me6C 6me7C 6me9C 1iroS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 51515.566 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.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium pasteurianum (bacteria) Gene: cybC, MTNR1B / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P0ABE7, UniProt: P49286, UniProt: P00268 #2: Chemical | #3: Chemical | ChemComp-ZN / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 68 % |
---|---|
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 |
---|---|
Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å |
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: 3.1→22 Å / Num. obs: 26228 / % possible obs: 100 % / Redundancy: 133 % / Biso Wilson estimate: 76.61 Å2 / R split: 0.19 / Net I/σ(I): 3.87 |
Reflection shell | Resolution: 3.1→3.23 Å / Num. unique obs: 3025 |
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 pump |
Serial crystallography data reduction | Crystal hits: 22267 / Frames indexed: 20704 / Frames total: 293060 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB id:1IRO Resolution: 3.1→22 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.876 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.327 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.937 / SU Rfree Blow DPI: 0.372 / SU Rfree Cruickshank DPI: 0.391
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 130.74 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 1.01 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.1→22 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1→3.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
|