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Yorodumi- PDB-5ojk: Crystal structure of the human neuroligin 1 cholinesterase domain... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ojk | ||||||||||||||||||||||||||||||||||||||||||
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Title | Crystal structure of the human neuroligin 1 cholinesterase domain containing spliced sequence B (SSB) (NL1(-A+B)) | ||||||||||||||||||||||||||||||||||||||||||
Components | Neuroligin-1,Neuroligin-1 | ||||||||||||||||||||||||||||||||||||||||||
Keywords | CELL ADHESION / neuroligin-neurexin / synaptic organizer protein / spliced sequence B | ||||||||||||||||||||||||||||||||||||||||||
Function / homology | Function and homology information neurexin clustering involved in presynaptic membrane assembly / asymmetric, glutamatergic, excitatory synapse / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuronal signal transduction / terminal button organization / neuron to neuron synapse ...neurexin clustering involved in presynaptic membrane assembly / asymmetric, glutamatergic, excitatory synapse / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuronal signal transduction / terminal button organization / neuron to neuron synapse / positive regulation of synaptic vesicle exocytosis / postsynaptic density protein 95 clustering / excitatory synapse assembly / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / presynaptic membrane assembly / synapse maturation / NMDA glutamate receptor clustering / maintenance of synapse structure / synaptic vesicle targeting / synaptic vesicle clustering / receptor localization to synapse / inhibitory synapse / neuron cell-cell adhesion / neurexin family protein binding / AMPA glutamate receptor clustering / presynapse assembly / filopodium tip / protein localization to synapse / neuron projection arborization / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of AMPA receptor activity / postsynaptic specialization membrane / Neurexins and neuroligins / positive regulation of synapse assembly / positive regulation of ruffle assembly / positive regulation of dendritic spine development / positive regulation of intracellular signal transduction / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron differentiation / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic vesicle endocytosis / GABA-ergic synapse / protein targeting / synaptic cleft / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / PDZ domain binding / positive regulation of synaptic transmission, GABAergic / modulation of chemical synaptic transmission / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / neuron projection development / rhythmic process / presynapse / signaling receptor activity / amyloid-beta binding / nervous system development / chemical synaptic transmission / postsynaptic membrane / postsynapse / scaffold protein binding / dendritic spine / postsynaptic density / receptor complex / dendrite / glutamatergic synapse / synapse / Golgi apparatus / cell surface / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||||||||||||||||||||||||||||||||||||||
Authors | Elegheert, J. / Aricescu, A.R. | ||||||||||||||||||||||||||||||||||||||||||
Funding support | United Kingdom, Canada, United States, 13items
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Citation | Journal: Neuron / Year: 2017 Title: Structural Mechanism for Modulation of Synaptic Neuroligin-Neurexin Signaling by MDGA Proteins. Authors: Elegheert, J. / Cvetkovska, V. / Clayton, A.J. / Heroven, C. / Vennekens, K.M. / Smukowski, S.N. / Regan, M.C. / Jia, W. / Smith, A.C. / Furukawa, H. / Savas, J.N. / de Wit, J. / Begbie, J. ...Authors: Elegheert, J. / Cvetkovska, V. / Clayton, A.J. / Heroven, C. / Vennekens, K.M. / Smukowski, S.N. / Regan, M.C. / Jia, W. / Smith, A.C. / Furukawa, H. / Savas, J.N. / de Wit, J. / Begbie, J. / Craig, A.M. / Aricescu, A.R. | ||||||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ojk.cif.gz | 224.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ojk.ent.gz | 176.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ojk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojk ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojk | HTTPS FTP |
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-Related structure data
Related structure data | 5oj2C 5oj6C 3bixS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 65559.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NLGN1, KIAA1070 / Plasmid: pHLsec / Cell line (production host): HEK293S GnTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q8N2Q7 #2: Sugar | #3: Chemical | ChemComp-PGE / #4: 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: 2.39 Å3/Da / Density % sol: 48.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M KSCN, 0.1M Bis-tris propane pH 8.5, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→51.7 Å / Num. obs: 40826 / % possible obs: 97.3 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rpim(I) all: 0.068 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.55→2.62 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3077 / CC1/2: 0.541 / Rpim(I) all: 0.484 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BIX Resolution: 2.55→51.7 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.46
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→51.7 Å
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Refine LS restraints |
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LS refinement shell |
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