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- PDB-5l2e: Crystal structure of rat Glutamate receptor delta-2 extracellular... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l2e | ||||||
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Title | Crystal structure of rat Glutamate receptor delta-2 extracellular domain | ||||||
![]() | Glutamate receptor ionotropic, delta-2,Glutamate receptor ionotropic, delta-2 | ||||||
![]() | PROTEIN BINDING / Synapse Protein / Cell Surface Protein / Glycoprotein / Nervous System | ||||||
Function / homology | ![]() excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly ...excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / regulation of postsynaptic density assembly / glutamate receptor activity / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of neuron projection development / regulation of presynapse assembly / ionotropic glutamate receptor complex / prepulse inhibition / regulation of neuron apoptotic process / somatodendritic compartment / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / modulation of chemical synaptic transmission / protein localization / scaffold protein binding / postsynaptic membrane / dendritic spine / glutamatergic synapse / synapse / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cheng, S. / Ozkan, E. | ||||||
![]() | ![]() Title: Conformational Plasticity in the Transsynaptic Neurexin-Cerebellin-Glutamate Receptor Adhesion Complex. Authors: Cheng, S. / Seven, A.B. / Wang, J. / Skiniotis, G. / Ozkan, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 384.5 KB | Display | ![]() |
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PDB format | ![]() | 314.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5kwrC ![]() 2vt3S ![]() 5kc8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 77833.812 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.09 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.1 M Sodium cacodylate pH 6.6, 1.3 M Ammonium dihydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2016 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.49 |
Reflection | Resolution: 4.15→50 Å / Num. obs: 30494 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.157 / Rsym value: 0.157 / Net I/av σ(I): 8.9 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 4.15→4.22 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.457 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2VT3 and 5KC8 Resolution: 4.152→46.583 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.5 Details: Refined with twin law -h,-k,l and twin fraction of 0.49.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.152→46.583 Å
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Refine LS restraints |
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LS refinement shell |
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