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Yorodumi- PDB-3uon: Structure of the human M2 muscarinic acetylcholine receptor bound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uon | ||||||
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Title | Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist | ||||||
Components | Human M2 muscarinic acetylcholine, receptor T4 lysozyme fusion protein | ||||||
Keywords | SIGNALING PROTEIN/ANTAGONIST / G protein-coupled receptor / GPCR / acetylcholine receptor / SIGNALING PROTEIN-ANTAGONIST 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 / viral release from host cell by cytolysis / presynaptic modulation of chemical synaptic transmission / peptidoglycan catabolic process / clathrin-coated endocytic vesicle membrane / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / lysozyme / Clathrin-mediated endocytosis / lysozyme activity / nervous system development / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / host cell cytoplasm / defense response to bacterium / G protein-coupled receptor signaling pathway / dendrite / neuronal cell body / glutamatergic synapse / synapse / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Haga, K. / Kruse, A.C. / Asada, H. / Yurugi-Kobayashi, T. / Shiroishi, M. / Zhang, C. / Weis, W.I. / Okada, T. / Kobilka, B.K. / Haga, T. / Kobayashi, T. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist. Authors: Haga, K. / Kruse, A.C. / Asada, H. / Yurugi-Kobayashi, T. / Shiroishi, M. / Zhang, C. / Weis, W.I. / Okada, T. / Kobilka, B.K. / Haga, T. / Kobayashi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uon.cif.gz | 103.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uon.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 3uon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uo/3uon ftp://data.pdbj.org/pub/pdb/validation_reports/uo/3uon | HTTPS FTP |
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-Related structure data
Related structure data | 2rh1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological molecule is equivalent to the contents of the asymmetric unit excluding the T4 lysozyme, which is a non-physiological crystallization aid. |
-Components
#1: Protein | Mass: 52694.543 Da / Num. of mol.: 1 Fragment: UNP RESIDUES 1-217, UNP RESIDUES 2-161, UNP RESIDUES 377-466 Mutation: N2D, N3D, N6D, N9D, C54T, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus) Gene: CHRM2, E / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08172, UniProt: P00720, lysozyme | ||||
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#2: Chemical | ChemComp-QNB / ( | ||||
#3: Sugar | ChemComp-BGC / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED TO ...THE STRUCTURE IS AN INTERNAL FUSION PROTEIN WITH LYSOZYME. AN OFFSET 1000 HAS BEEN ADDED TO ORIGINAL SEQUENCE DATABASE RESIDUE NUMBERS (2-161) OF THE LYSOZYME PART IN COORDINATE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 23 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 25 to 35% PEG 300, 100 mM ammonium phosphate, 2% 2-Methyl-2,4-pentanediol, 100 mM HEPES, 10:1 monoolein:cholesterol lipid mix diluted 1.5:1 with protein in detergent buffer, Lipidic cubic ...Details: 25 to 35% PEG 300, 100 mM ammonium phosphate, 2% 2-Methyl-2,4-pentanediol, 100 mM HEPES, 10:1 monoolein:cholesterol lipid mix diluted 1.5:1 with protein in detergent buffer, Lipidic cubic phase, temperature 293K, pH 7.5 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 3→27.5 Å / Num. obs: 11726 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 6.1 | ||||||||||||||||||
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 1.4 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Beta2 adrenergic receptor, T4 lysozyme (PDB ENTRY 2RH1) Resolution: 3→27.466 Å / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.16 Å / VDW probe radii: 0.5 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.88 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3→27.466 Å
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Refine LS restraints |
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