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Yorodumi- PDB-3biw: Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3biw | |||||||||
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Title | Crystal structure of the Neuroligin-1/Neurexin-1beta synaptic adhesion complex | |||||||||
Components |
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Keywords | Cell adhesion/Cell adhesion / protein-protein complex / esterase domain / LNS domain / alpha-beta hydrolase / Cell adhesion / Cell junction / Glycoprotein / Membrane / Postsynaptic cell membrane / Synapse / Transmembrane / Alternative promoter usage / Cell adhesion-Cell adhesion COMPLEX | |||||||||
Function / homology | Function and homology information trans-synaptic signaling by endocannabinoid / neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / : / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness ...trans-synaptic signaling by endocannabinoid / neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / : / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cytoskeletal matrix organization at active zone / cell-cell adhesion involved in synapse maturation / positive regulation of circadian sleep/wake cycle, wakefulness / retrograde trans-synaptic signaling by trans-synaptic protein complex / gephyrin clustering involved in postsynaptic density assembly / regulation of postsynaptic specialization assembly / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / type 1 fibroblast growth factor receptor binding / terminal button organization / neuron to neuron synapse / positive regulation of synaptic vesicle exocytosis / neuroligin clustering involved in postsynaptic membrane assembly / : / postsynaptic density protein 95 clustering / excitatory synapse assembly / cerebellar granule cell differentiation / postsynaptic specialization assembly / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / neuronal ion channel clustering / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / synapse maturation / NMDA glutamate receptor clustering / maintenance of synapse structure / negative regulation of filopodium assembly / Neurexins and neuroligins / neuroligin family protein binding / vocal learning / positive regulation of synapse maturation / synaptic vesicle targeting / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of postsynaptic density assembly / synaptic membrane adhesion / synaptic vesicle clustering / receptor localization to synapse / inhibitory synapse / regulation of grooming behavior / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / AMPA glutamate receptor clustering / presynapse assembly / filopodium tip / protein localization to synapse / regulation of synaptic vesicle cycle / vocalization behavior / neuron projection arborization / positive regulation of synaptic vesicle endocytosis / regulation of insulin secretion involved in cellular response to glucose stimulus / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / vesicle docking involved in exocytosis / neurotransmitter secretion / regulation of AMPA receptor activity / filopodium assembly / neuron maturation / postsynaptic specialization membrane / acetylcholine receptor binding / positive regulation of synapse assembly / positive regulation of ruffle assembly / positive regulation of protein kinase C activity / positive regulation of dendritic spine development / positive regulation of protein localization to synapse / positive regulation of intracellular signal transduction / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / synaptic vesicle transport / regulation of neuron differentiation / adult behavior / positive regulation of protein kinase A signaling / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / calcium channel regulator activity / neuromuscular process controlling balance / excitatory synapse / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / GABA-ergic synapse / protein targeting / synaptic cleft / prepulse inhibition / axonal growth cone / presynaptic active zone membrane / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å | |||||||||
Authors | Arac, D. / Boucard, A.A. / Ozkan, E. / Strop, P. / Newell, E. / Sudhof, T.C. / Brunger, A.T. | |||||||||
Citation | Journal: Neuron / Year: 2007 Title: Structures of Neuroligin-1 and the Neuroligin-1/Neurexin-1beta Complex Reveal Specific Protein-Protein and Protein-Ca(2+) Interactions. Authors: Arac, D. / Boucard, A.A. / Ozkan, E. / Strop, P. / Newell, E. / Sudhof, T.C. / Brunger, A.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3biw.cif.gz | 541.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3biw.ent.gz | 446.8 KB | Display | PDB format |
PDBx/mmJSON format | 3biw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bi/3biw ftp://data.pdbj.org/pub/pdb/validation_reports/bi/3biw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Details | The biological assembly is a heterotetramer of two Neurexin-1beta molecules bound to a Neuroligin-1 dimer. |
-Components
#1: Protein | Mass: 64228.961 Da / Num. of mol.: 4 / Fragment: extracellular esterase domain of Neuroligin-1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nlgn1 / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q62765 #2: Protein | Mass: 26030.043 Da / Num. of mol.: 4 / Fragment: extracellular LNS domain of Neurexin-1beta Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nrxn1 / Plasmid: pAcGP67A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q63373, UniProt: Q63372*PLUS #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Chemical | ChemComp-CA / |
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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: 2.93 Å3/Da / Density % sol: 57.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 8% PEG6000, 0.1 M MgCl2, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 130 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.41→50 Å / Num. obs: 53484 / % possible obs: 92.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Χ2: 1.042 / Net I/σ(I): 9.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→45.9 Å / Rfactor Rfree error: 0.005 / FOM work R set: 0.785 / Data cutoff high absF: 3736422 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.015 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 133.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→45.9 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 3.5→3.72 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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