+Open data
-Basic information
Entry | Database: PDB / ID: 3b3q | |||||||||
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Title | Crystal structure of a synaptic adhesion complex | |||||||||
Components |
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Keywords | CELL ADHESION / synaptic formation / adhesion / heterophilic / protein-protein complex / calcium binding / Membrane / Transmembrane | |||||||||
Function / homology | Function and homology information neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / : / 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 ...neurexin clustering involved in presynaptic membrane assembly / regulation of presynapse organization / protein-containing complex assembly involved in synapse maturation / : / 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 / Neurexins and neuroligins / 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 / neuronal signal transduction / neuroligin clustering involved in postsynaptic membrane assembly / excitatory synapse assembly / postsynaptic density protein 95 clustering / cerebellar granule cell differentiation / negative regulation of dendritic spine morphogenesis / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / positive regulation of synaptic vesicle clustering / presynaptic membrane assembly / synapse maturation / negative regulation of filopodium assembly / maintenance of synapse structure / synaptic vesicle targeting / neuroligin family protein binding / positive regulation of fibroblast growth factor receptor signaling pathway / synaptic membrane adhesion / synaptic vesicle clustering / inhibitory synapse / receptor localization to synapse / neuron cell-cell adhesion / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / filopodium tip / protein localization to synapse / NMDA glutamate receptor clustering / neuron projection arborization / vocalization behavior / positive regulation of synaptic vesicle endocytosis / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of AMPA receptor activity / AMPA glutamate receptor clustering / Neurexins and neuroligins / NMDA selective glutamate receptor complex / positive regulation of synapse assembly / positive regulation of ruffle assembly / positive regulation of protein kinase C activity / positive regulation of filopodium assembly / positive regulation of protein localization to synapse / positive regulation of intracellular signal transduction / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / synaptic vesicle transport / regulation of neuron differentiation / adult behavior / positive regulation of dendritic spine development / positive regulation of protein kinase A signaling / plasma membrane => GO:0005886 / regulation of NMDA receptor activity / social behavior / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic vesicle endocytosis / endocytic vesicle / protein targeting / GABA-ergic synapse / axonal growth cone / synaptic cleft / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / dendritic shaft / learning / long-term synaptic potentiation / PDZ domain binding / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / synapse organization / modulation of chemical synaptic transmission / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / calcium-dependent protein binding / neuron projection development / rhythmic process / transmembrane signaling receptor activity / presynapse / signaling receptor activity / presynaptic membrane / positive regulation of peptidyl-serine phosphorylation / nervous system development Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Chen, X. / Liu, H. / Shim, A. / Focia, P. / He, X. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2008 Title: Structural basis for synaptic adhesion mediated by neuroligin-neurexin interactions. Authors: Chen, X. / Liu, H. / Shim, A.H. / Focia, P.J. / He, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b3q.cif.gz | 334.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b3q.ent.gz | 264.7 KB | Display | PDB format |
PDBx/mmJSON format | 3b3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/3b3q ftp://data.pdbj.org/pub/pdb/validation_reports/b3/3b3q | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABEF
#1: Protein | Mass: 64623.363 Da / Num. of mol.: 2 / Fragment: cholinesterase-like domain / Mutation: N343Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlgn1 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4KMN5, UniProt: Q99K10*PLUS #2: Protein | Mass: 21457.939 Da / Num. of mol.: 2 / Fragment: LNS domain or LG domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRXN1 / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4FVB9, UniProt: P58400*PLUS |
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-Sugars , 2 types, 4 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 1554 molecules
#5: Chemical | #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: 2.8 Å3/Da / Density % sol: 56.06 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1M sodium citrate, 0.1M sodium cacodylate, 0.2M sodium chloride, 0.01M calcium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 76375 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.2 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1N5M and 1C4R Resolution: 2.4→24.64 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 62.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→24.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015
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