+Open data
-Basic information
Entry | Database: PDB / ID: 4daj | ||||||
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Title | Structure of the M3 Muscarinic Acetylcholine Receptor | ||||||
Components | Muscarinic acetylcholine receptor M3, Lysozyme | ||||||
Keywords | SIGNALING PROTEIN / Hydrolase / G protein-coupled receptor / muscarinic receptor / Acetylcholine receptor | ||||||
Function / homology | Function and homology information negative regulation of heart rate by acetylcholine / G protein-coupled acetylcholine receptor binding / Muscarinic acetylcholine receptors / regulation of vascular associated smooth muscle contraction / saliva secretion / quaternary ammonium group binding / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / G protein-coupled acetylcholine receptor activity ...negative regulation of heart rate by acetylcholine / G protein-coupled acetylcholine receptor binding / Muscarinic acetylcholine receptors / regulation of vascular associated smooth muscle contraction / saliva secretion / quaternary ammonium group binding / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / response to acetylcholine / G protein-coupled acetylcholine receptor activity / positive regulation of vascular associated smooth muscle contraction / adenylate cyclase-inhibiting G protein-coupled acetylcholine receptor signaling pathway / positive regulation of smooth muscle contraction / G protein-coupled serotonin receptor activity / synaptic transmission, cholinergic / acetylcholine binding / G alpha (q) signalling events / acetylcholine receptor signaling pathway / ligand-gated ion channel signaling pathway / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / asymmetric synapse / smooth muscle contraction / axon terminus / viral release from host cell by cytolysis / positive regulation of vasoconstriction / peptidoglycan catabolic process / basal plasma membrane / calcium-mediated signaling / postsynaptic density membrane / positive regulation of insulin secretion / G protein-coupled acetylcholine receptor signaling pathway / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / presynaptic membrane / chemical synaptic transmission / basolateral plasma membrane / host cell cytoplasm / defense response to bacterium / glutamatergic synapse / synapse / dendrite / endoplasmic reticulum membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Kruse, A.C. / Hu, J. / Pan, A.C. / Arlow, D.H. / Rosenbaum, D.M. / Rosemond, E. / Green, H.F. / Liu, T. / Chae, P.S. / Dror, R.O. ...Kruse, A.C. / Hu, J. / Pan, A.C. / Arlow, D.H. / Rosenbaum, D.M. / Rosemond, E. / Green, H.F. / Liu, T. / Chae, P.S. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Wess, J. / Kobilka, B. | ||||||
Citation | Journal: Nature / Year: 2012 Title: Structure and dynamics of the M3 muscarinic acetylcholine receptor. Authors: Kruse, A.C. / Hu, J. / Pan, A.C. / Arlow, D.H. / Rosenbaum, D.M. / Rosemond, E. / Green, H.F. / Liu, T. / Chae, P.S. / Dror, R.O. / Shaw, D.E. / Weis, W.I. / Wess, J. / Kobilka, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4daj.cif.gz | 345.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4daj.ent.gz | 279.3 KB | Display | PDB format |
PDBx/mmJSON format | 4daj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4daj_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4daj_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4daj_validation.xml.gz | 67.5 KB | Display | |
Data in CIF | 4daj_validation.cif.gz | 88.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/4daj ftp://data.pdbj.org/pub/pdb/validation_reports/da/4daj | HTTPS FTP |
-Related structure data
Related structure data | 3uonS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 54990.297 Da / Num. of mol.: 4 Fragment: P08483 residues 57-259, 482-589, P00720 residues 1-161 Mutation: C1054T, C1097A Source method: isolated from a genetically manipulated source Details: Chimeric Protein Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Enterobacteria phage T4 (virus) Gene: Chrm-3, Chrm3, E / Plasmid: PVL1392 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P08483, UniProt: P00720, lysozyme #2: Chemical | ChemComp-0HK / ( #3: Chemical | ChemComp-PO4 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 76 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.17 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 27-38% PEG 300, 100 mM HEPES pH 7.5, 1% (w/w) 1,2,3-heptanetriol, and 100 mM ammonium phosphate. Protein was reconstituted in cubic phase using a 10:1 monolein:cholesterol mix by weight, ...Details: 27-38% PEG 300, 100 mM HEPES pH 7.5, 1% (w/w) 1,2,3-heptanetriol, and 100 mM ammonium phosphate. Protein was reconstituted in cubic phase using a 10:1 monolein:cholesterol mix by weight, Lipidic cubic phase, temperature 293K |
-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: 3.4→40 Å / Num. obs: 28385 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.226 / Net I/σ(I): 4.5 | ||||||||||||||||||
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 1.7 / % possible all: 85.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: M2 muscarinic acetylcholine receptor (3UON) Resolution: 3.4→39.9 Å / SU ML: 0.59 / σ(F): 1.98 / Phase error: 33.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.27 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.36 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.4→39.9 Å
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Refine LS restraints |
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LS refinement shell |
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