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Yorodumi- PDB-3bl8: Crystal structure of the extracellular domain of neuroligin 2A fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bl8 | |||||||||
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Title | Crystal structure of the extracellular domain of neuroligin 2A from mouse | |||||||||
Components | Neuroligin-2 | |||||||||
Keywords | CELL ADHESION / neuroligin 2A / Glycoprotein / Membrane / Phosphoprotein / Transmembrane | |||||||||
Function / homology | Function and homology information jump response / positive regulation of t-SNARE clustering / : / : / gephyrin clustering involved in postsynaptic density assembly / Neurexins and neuroligins / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic specialization assembly / postsynaptic membrane assembly ...jump response / positive regulation of t-SNARE clustering / : / : / gephyrin clustering involved in postsynaptic density assembly / Neurexins and neuroligins / terminal button organization / postsynaptic density protein 95 clustering / postsynaptic specialization assembly / postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / positive regulation of inhibitory postsynaptic potential / thigmotaxis / ribbon synapse / inhibitory synapse / dopaminergic synapse / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / insulin metabolic process / protein localization to synapse / inhibitory synapse assembly / glycinergic synapse / regulation of AMPA receptor activity / positive regulation of synapse assembly / positive regulation of dendritic spine development / positive regulation of protein localization to synapse / locomotory exploration behavior / plasma membrane => GO:0005886 / social behavior / positive regulation of excitatory postsynaptic potential / neuromuscular process controlling balance / excitatory synapse / regulation of presynapse assembly / synaptic vesicle endocytosis / GABA-ergic synapse / sensory perception of pain / synapse assembly / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / positive regulation of synaptic transmission, GABAergic / synapse organization / modulation of chemical synaptic transmission / positive regulation of insulin secretion / signaling receptor activity / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / synapse / positive regulation of cell population proliferation / cell surface / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å | |||||||||
Authors | Jin, X. / Koehnke, J. / Shapiro, L. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Authors: Koehnke, J. / Jin, X. / Budreck, E.C. / Posy, S. / Scheiffele, P. / Honig, B. / Shapiro, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bl8.cif.gz | 416.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bl8.ent.gz | 350.5 KB | Display | PDB format |
PDBx/mmJSON format | 3bl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3bl8 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bl8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 64850.801 Da / Num. of mol.: 4 / Fragment: esterase-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn2, Kiaa1366 / Plasmid: pCEP4-NL2A / Cell line (production host): HEK293-GNTI / Production host: Homo sapiens (human) / References: UniProt: Q69ZK9 #2: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | #5: 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: 3.57 Å3/Da / Density % sol: 65.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 3.5% PEG 6000, 0.1M Bicine, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 7, 2007 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. all: 57279 / Num. obs: 54385 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Χ2: 1.003 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 3.3→3.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.4 / Num. unique all: 5279 / Rsym value: 0.503 / Χ2: 1.015 / % possible all: 96.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 61.915 / SU ML: 0.467 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 126.202 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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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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