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Yorodumi- PDB-4ey8: Crystal structure of recombinant human acetylcholinesterase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ey8 | |||||||||
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Title | Crystal structure of recombinant human acetylcholinesterase in complex with fasciculin-2 | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / acetylcholinesterase / hydrolase / fasciculin 2 / snake venom toxin / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway ...negative regulation of synaptic transmission, cholinergic / Neurotransmitter clearance / acetylcholine catabolic process in synaptic cleft / cholinesterase activity / serine hydrolase activity / acetylcholine catabolic process / acetylcholine binding / amyloid precursor protein metabolic process / acetylcholinesterase / acetylcholine receptor signaling pathway / osteoblast development / acetylcholinesterase activity / choline metabolic process / Synthesis of PC / basement membrane / regulation of receptor recycling / Synthesis, secretion, and deacylation of Ghrelin / side of membrane / synaptic cleft / laminin binding / synapse assembly / collagen binding / positive regulation of protein secretion / neuromuscular junction / receptor internalization / : / retina development in camera-type eye / nervous system development / positive regulation of cold-induced thermogenesis / amyloid-beta binding / toxin activity / hydrolase activity / cell adhesion / synapse / perinuclear region of cytoplasm / Golgi apparatus / cell surface / protein homodimerization activity / extracellular space / extracellular region / membrane / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Dendroaspis angusticeps (eastern green mamba) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5958 Å | |||||||||
Authors | Cheung, J. / Rudolph, M. / Burshteyn, F. / Cassidy, M. / Gary, E. / Love, J. / Height, J. / Franklin, M. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2012 Title: Structures of human acetylcholinesterase in complex with pharmacologically important ligands. Authors: Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M.S. / Gary, E.N. / Love, J. / Franklin, M.C. / Height, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ey8.cif.gz | 132.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ey8.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ey8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ey8_validation.pdf.gz | 809.1 KB | Display | wwPDB validaton report |
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Full document | 4ey8_full_validation.pdf.gz | 814.5 KB | Display | |
Data in XML | 4ey8_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 4ey8_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/4ey8 ftp://data.pdbj.org/pub/pdb/validation_reports/ey/4ey8 | HTTPS FTP |
-Related structure data
Related structure data | 4ey4C 4ey5C 4ey6C 4ey7C 1b41S S: Starting model for refinement C: citing same article (ref.) |
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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 | dimer |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 59447.105 Da / Num. of mol.: 1 / Fragment: UNP Residues 33-574 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ACHE / Production host: Homo sapiens (human) / Tissue (production host): HEK-293 / References: UniProt: P22303, acetylcholinesterase |
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#2: Protein | Mass: 6768.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Dendroaspis angusticeps (eastern green mamba) Secretion: VENOM / References: UniProt: P0C1Z0 |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 48 molecules
#4: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.32 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop Details: 1.6 to 2.0M ammonium sulphate, 0.1M HEPES pH 7.5 - 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 283K PH range: 7.5 - 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.99 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5958→50 Å / Num. all: 34182 / Num. obs: 33704 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 11.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1b41 Resolution: 2.5958→46.381 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.35 / σ(F): 0 / Phase error: 30.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5958→46.381 Å
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Refine LS restraints |
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LS refinement shell |
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