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- PDB-1c4r: THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REG... -
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Basic information
Entry | Database: PDB / ID: 1c4r | ||||||
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Title | THE STRUCTURE OF THE LIGAND-BINDING DOMAIN OF NEUREXIN 1BETA: REGULATION OF LNS DOMAIN FUNCTION BY ALTERNATIVE SPLICING | ||||||
![]() | NEUREXIN-I BETA | ||||||
![]() | MEMBRANE PROTEIN / LECTIN-LIKE / NEUROBIOLOGY / CELL-CELL ADHESION / CELL-CELL RECOGNITION / ALTERNATIVE SPLICING | ||||||
Function / homology | ![]() 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 / cell-cell adhesion involved in synapse maturation / regulation of postsynaptic specialization assembly / protein complex involved in cell-cell adhesion / gephyrin clustering involved in postsynaptic density assembly / type 1 fibroblast growth factor receptor binding / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering ...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 / cell-cell adhesion involved in synapse maturation / regulation of postsynaptic specialization assembly / protein complex involved in cell-cell adhesion / gephyrin clustering involved in postsynaptic density assembly / type 1 fibroblast growth factor receptor binding / positive regulation of neuromuscular synaptic transmission / guanylate kinase-associated protein clustering / 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 / negative regulation of filopodium assembly / maintenance of synapse structure / vocal learning / neuroligin family protein binding / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of synapse maturation / regulation of postsynaptic density assembly / inhibitory synapse / synaptic vesicle clustering / neuron cell-cell adhesion / synaptic membrane adhesion / regulation of grooming behavior / presynapse assembly / receptor localization to synapse / protein localization to synapse / NMDA glutamate receptor clustering / vocalization behavior / regulation of synaptic vesicle cycle / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / neurotransmitter secretion / regulation of AMPA receptor activity / filopodium assembly / neuron maturation / acetylcholine receptor binding / positive regulation of synapse assembly / regulation of NMDA receptor activity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / adult behavior / positive regulation of protein kinase A signaling / positive regulation of excitatory postsynaptic potential / social behavior / neuromuscular process controlling balance / regulation of presynapse assembly / endocytic vesicle / excitatory synapse / calcium channel regulator activity / GABA-ergic synapse / prepulse inhibition / axonal growth cone / presynaptic active zone membrane / cell adhesion molecule binding / synapse assembly / cellular response to calcium ion / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / learning / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / establishment of protein localization / neuromuscular junction / Schaffer collateral - CA1 synapse / positive regulation of neuron projection development / circadian rhythm / transmembrane signaling receptor activity / calcium-dependent protein binding / neuron projection development / positive regulation of peptidyl-serine phosphorylation / presynaptic membrane / chemical synaptic transmission / nuclear membrane / angiogenesis / vesicle / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of gene expression / signaling receptor binding / neuronal cell body / glutamatergic synapse / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / cell surface / signal transduction / endoplasmic reticulum / protein-containing complex / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Rudenko, G. / Nguyen, T. / Chelliah, Y. / Sudhof, T.C. / Deisenhofer, J. | ||||||
![]() | ![]() Title: The structure of the ligand-binding domain of neurexin Ibeta: regulation of LNS domain function by alternative splicing. Authors: Rudenko, G. / Nguyen, T. / Chelliah, Y. / Sudhof, T.C. / Deisenhofer, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.7 KB | Display | ![]() |
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PDB format | ![]() | 226.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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8 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 19693.072 Da / Num. of mol.: 8 / Fragment: EXTRACELLULAR DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Biso Wilson estimate: 29.3 Å2 | |||||||||||||||
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. obs: 73128 / % possible obs: 98.1 % / Num. measured all: 351083 / Rmerge(I) obs: 0.095 | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.64 Å / % possible obs: 82.7 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 3.1 |
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Processing
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Refinement | Resolution: 2.6→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.87 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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