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Yorodumi- PDB-5zk3: Crystal structure of rationally thermostabilized M2 muscarinic ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zk3 | |||||||||||||||||||||
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Title | Crystal structure of rationally thermostabilized M2 muscarinic acetylcholine receptor bound with QNB | |||||||||||||||||||||
Components | Muscarinic acetylcholine receptor M2,Apo-cytochrome b562,Muscarinic acetylcholine receptor M2 | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN/INHIBITOR / GPCR crystallography / rationally thermostabilized mutant / MEMBRANE PROTEIN-INHIBITOR complex | |||||||||||||||||||||
Function / homology | Function and homology information Muscarinic acetylcholine receptors / symmetric synapse / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled acetylcholine receptor activity / regulation of smooth muscle contraction / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / arrestin family protein binding / regulation of heart contraction ...Muscarinic acetylcholine receptors / symmetric synapse / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled acetylcholine receptor activity / regulation of smooth muscle contraction / cholinergic synapse / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / G protein-coupled serotonin receptor activity / arrestin family protein binding / regulation of heart contraction / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / asymmetric synapse / axon terminus / presynaptic modulation of chemical synaptic transmission / clathrin-coated endocytic vesicle membrane / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / nervous system development / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / G protein-coupled receptor signaling pathway / neuronal cell body / dendrite / synapse / glutamatergic synapse / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||||||||||||||
Authors | Suno, R. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. ...Suno, R. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / Iwata, S. / Kobayashi, T. | |||||||||||||||||||||
Funding support | Japan, United States, 6items
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Citation | Journal: Nat. Chem. Biol. / Year: 2018 Title: Structural insights into the subtype-selective antagonist binding to the M2muscarinic receptor Authors: Suno, R. / Lee, S. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / ...Authors: Suno, R. / Lee, S. / Maeda, S. / Yasuda, S. / Yamashita, K. / Hirata, K. / Horita, S. / Tawaramoto, M.S. / Tsujimoto, H. / Murata, T. / Kinoshita, M. / Yamamoto, M. / Kobilka, B.K. / Vaidehi, N. / Iwata, S. / Kobayashi, T. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zk3.cif.gz | 164.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zk3.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zk3 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zk3 | HTTPS FTP |
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-Related structure data
Related structure data | 5yc8C 5zk8C 5zkbC 5zkcC 5xba 5xbb C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.1094808 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47293.207 Da / Num. of mol.: 1 / Fragment: UNP residues 10-217,UNP residues 377-466 / Mutation: S110R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHRM2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08172 |
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#2: Chemical | ChemComp-QNB / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.75 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 50mM MES-NaOH pH 6.2-7.0, 26-32% PEG300, 300~500mM Ammonium Fluoride, 1% 1,2,3-heptanetriol, 0.5mM QNB and 5% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Jul 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 14817 / % possible obs: 99.9 % / Redundancy: 12.7 % / Net I/σ(I): 8.28 |
Reflection shell | Resolution: 2.6→2.76 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.908 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45.908 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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