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- PDB-5kca: Crystal structure of the Cbln1 C1q domain trimer in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kca | ||||||
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Title | Crystal structure of the Cbln1 C1q domain trimer in complex with the amino-terminal domain (ATD) of iGluR Delta-2 (GluD2) | ||||||
![]() | Cerebellin-1,Cerebellin-1,Cerebellin-1,Glutamate receptor ionotropic, delta-2 | ||||||
![]() | SIGNALING PROTEIN / Cerebellin / ionotropic glutamate receptor (iGluR) / neurotransmission | ||||||
Function / homology | ![]() negative regulation of inhibitory synapse assembly / excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / maintenance of synapse structure / regulation of postsynaptic density assembly / negative regulation of excitatory postsynaptic potential / glutamate receptor signaling pathway / glutamate receptor activity / positive regulation of synapse assembly ...negative regulation of inhibitory synapse assembly / excitatory synapse assembly / cerebellar granule cell differentiation / positive regulation of long-term synaptic depression / maintenance of synapse structure / regulation of postsynaptic density assembly / negative regulation of excitatory postsynaptic potential / glutamate receptor signaling pathway / 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 / ionotropic glutamate receptor complex / regulation of presynapse assembly / protein secretion / prepulse inhibition / regulation of neuron apoptotic process / synaptic cleft / glutamate-gated receptor activity / synapse assembly / excitatory postsynaptic potential / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / PDZ domain binding / postsynaptic density membrane / synapse organization / modulation of chemical synaptic transmission / protein localization / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / collagen-containing extracellular matrix / dendritic spine / glutamatergic synapse / synapse / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elegheert, J. / Aricescu, A.R. | ||||||
![]() | ![]() Title: Structural basis for integration of GluD receptors within synaptic organizer complexes. Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / ...Authors: Elegheert, J. / Kakegawa, W. / Clay, J.E. / Shanks, N.F. / Behiels, E. / Matsuda, K. / Kohda, K. / Miura, E. / Rossmann, M. / Mitakidis, N. / Motohashi, J. / Chang, V.T. / Siebold, C. / Greger, I.H. / Nakagawa, T. / Yuzaki, M. / Aricescu, A.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175 KB | Display | ![]() |
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PDB format | ![]() | 133.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.8 KB | Display | ![]() |
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Full document | ![]() | 440.2 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 37 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kc5SC ![]() 5kc6C ![]() 5kc7C ![]() 5kc8SC ![]() 5kc9C 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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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) |
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Components
#1: Protein | Mass: 97237.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-CA / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 60% (v/v) tacsimate pH 7.0 (1.8305 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0. ...Details: 60% (v/v) tacsimate pH 7.0 (1.8305 M malonic acid, 0.25 M ammonium citrate tribasic, 0.12 M succinic acid, 0.3 M DL-malic acid, 0.4 M sodium acetate trihydrate, 0.5 M sodium formate, and 0.16 M ammonium tartrate dibasic) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→46.05 Å / Num. obs: 30725 / % possible obs: 99.6 % / Redundancy: 7.6 % / Biso Wilson estimate: 66.4 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.224 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.377 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5KC5, 5KC8 Resolution: 3.1→46.023 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→46.023 Å
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Refine LS restraints |
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LS refinement shell |
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