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Yorodumi- PDB-2r1d: Crystal structure of rat neurexin 1beta in the Ca2+ containing form -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2r1d | ||||||
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| Title | Crystal structure of rat neurexin 1beta in the Ca2+ containing form | ||||||
Components | Neurexin-1-beta | ||||||
Keywords | CELL ADHESION / SPLICING / beta-sandwich | ||||||
| Function / homology | Function and homology informationprotein-containing complex assembly involved in synapse maturation / : / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / guanylate kinase-associated protein clustering / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission ...protein-containing complex assembly involved in synapse maturation / : / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / guanylate kinase-associated protein clustering / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / neuroligin clustering involved in postsynaptic membrane assembly / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / type 1 fibroblast growth factor receptor binding / trans-synaptic signaling, modulating synaptic transmission / trans-synaptic protein complex / negative regulation of filopodium assembly / gephyrin clustering involved in postsynaptic density assembly / cerebellar granule cell differentiation / slit diaphragm / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / synapse maturation / gamma-aminobutyric acid receptor clustering / vocal learning / presynaptic membrane assembly / neuroligin family protein binding / positive regulation of synapse maturation / maintenance of synapse structure / regulation of grooming behavior / synaptic vesicle clustering / presynapse assembly / synaptic membrane adhesion / regulation of postsynaptic specialization assembly / positive regulation of fibroblast growth factor receptor signaling pathway / receptor localization to synapse / neuron cell-cell adhesion / NMDA glutamate receptor clustering / inhibitory synapse / calcium-dependent cell-cell adhesion / vocalization behavior / regulation of postsynaptic density assembly / protein localization to synapse / acetylcholine receptor binding / neurotransmitter secretion / regulation of synaptic vesicle cycle / AMPA selective glutamate receptor signaling pathway / positive regulation of synapse assembly / NMDA selective glutamate receptor signaling pathway / heterophilic cell-cell adhesion / neuromuscular process controlling balance / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / adult behavior / excitatory synapse / endocytic vesicle / social behavior / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / prepulse inhibition / positive regulation of synaptic transmission, glutamatergic / axonal growth cone / synapse assembly / cell adhesion molecule binding / neuron projection morphogenesis / presynaptic active zone membrane / cellular response to calcium ion / positive regulation of synaptic transmission, GABAergic / learning / positive regulation of protein localization to plasma membrane / calcium channel regulator activity / neuromuscular junction / establishment of protein localization / positive regulation of neuron projection development / circadian rhythm / GABA-ergic synapse / Schaffer collateral - CA1 synapse / neuron projection development / calcium-dependent protein binding / transmembrane signaling receptor activity / presynaptic membrane / angiogenesis / nuclear membrane / vesicle / chemical synaptic transmission / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signaling receptor binding / negative regulation of gene expression / neuronal cell body / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / signal transduction / protein-containing complex / plasma membrane Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Rudenko, G. | ||||||
Citation | Journal: Structure / Year: 2008Title: Regulation of Neurexin 1beta Tertiary Structure and Ligand Binding through Alternative Splicing Authors: Shen, K.C. / Kuczynska, D.A. / Wu, I.J. / Murray, B.H. / Sheckler, L.R. / Rudenko, G. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2r1d.cif.gz | 310.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2r1d.ent.gz | 249 KB | Display | PDB format |
| PDBx/mmJSON format | 2r1d.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2r1d_validation.pdf.gz | 518.5 KB | Display | wwPDB validaton report |
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| Full document | 2r1d_full_validation.pdf.gz | 546.6 KB | Display | |
| Data in XML | 2r1d_validation.xml.gz | 55.4 KB | Display | |
| Data in CIF | 2r1d_validation.cif.gz | 75.9 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/2r1d ftp://data.pdbj.org/pub/pdb/validation_reports/r1/2r1d | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2r16C ![]() 2r1bC ![]() 1c4rS C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Assembly
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| Noncrystallographic symmetry (NCS) | NCS domain:
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