+Open data
-Basic information
Entry | Database: PDB / ID: 2xb6 | ||||||
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Title | Revisited crystal structure of Neurexin1beta-Neuroligin4 complex | ||||||
Components |
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Keywords | CELL ADHESION / ALPHA-BETA-HYDROLASE FOLD / AUTISM / CONFORMATIONAL REARRANGEMENT | ||||||
Function / homology | Function and homology information asymmetric, glutamatergic, excitatory synapse / protein-containing complex assembly involved in synapse maturation / symmetric, GABA-ergic, inhibitory synapse / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / 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 ...asymmetric, glutamatergic, excitatory synapse / protein-containing complex assembly involved in synapse maturation / symmetric, GABA-ergic, inhibitory synapse / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / 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 / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / postsynaptic density protein 95 clustering / cerebellar granule cell differentiation / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / presynaptic membrane assembly / synapse maturation / NMDA glutamate receptor clustering / maintenance of synapse structure / negative regulation of filopodium assembly / neuroligin family protein binding / vocal learning / positive regulation of synapse maturation / 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 / brainstem development / neuron cell-cell adhesion / neurexin family protein binding / negative regulation of excitatory postsynaptic potential / presynapse assembly / protein localization to synapse / regulation of synaptic vesicle cycle / vocalization behavior / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / neurotransmitter secretion / cell-cell junction organization / regulation of AMPA receptor activity / filopodium assembly / neuron maturation / acetylcholine receptor binding / Neurexins and neuroligins / positive regulation of synapse assembly / chloride ion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / organ growth / 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 / prepulse inhibition / axonal growth cone / presynaptic active zone membrane / synapse assembly / cellular response to calcium ion / cell adhesion molecule binding / cerebellum development / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / learning / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / synapse organization / positive regulation of protein localization to plasma membrane / modulation of chemical synaptic transmission / neuromuscular junction / Schaffer collateral - CA1 synapse / establishment of protein localization / positive regulation of neuron projection development / neuron differentiation / circadian rhythm / neuron projection development / calcium-dependent protein binding / transmembrane signaling receptor activity / presynapse / signaling receptor activity / presynaptic membrane / positive regulation of peptidyl-serine phosphorylation / chemical synaptic transmission / scaffold protein binding / angiogenesis / nuclear membrane / vesicle / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Leone, P. / Comoletti, D. / Ferracci, G. / Conrod, S. / Garcia, S.U. / Taylor, P. / Bourne, Y. / Marchot, P. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Structural Insights Into the Exquisite Selectivity of Neurexin-Neuroligin Synaptic Interactions Authors: Leone, P. / Comoletti, D. / Ferracci, G. / Conrod, S. / Garcia, S.U. / Taylor, P. / Bourne, Y. / Marchot, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xb6.cif.gz | 299.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xb6.ent.gz | 240.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/2xb6 ftp://data.pdbj.org/pub/pdb/validation_reports/xb/2xb6 | HTTPS FTP |
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-Related structure data
Related structure data | 2wqzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 66230.203 Da / Num. of mol.: 2 / Fragment: CHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q8N0W4 #2: Protein | Mass: 19367.713 Da / Num. of mol.: 2 / Fragment: LNS DOMAIN, RESIDUES 80-258 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q63373 |
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-Sugars , 1 types, 4 molecules
#3: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 387 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-MES / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | R561K IS A SPONTANEOU |
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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: 3.2 Å3/Da / Density % sol: 59 % / Description: NONE |
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Crystal grow | pH: 6.3 / Details: 100MM MES PH6.3,10% PEG 20000, 2MM CACL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9834 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9834 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 72526 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WQZ Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.938 / SU ML: 0.182 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.394 / ESU R Free: 0.258 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.92 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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