+
Open data
-
Basic information
Entry | Database: PDB / ID: 5kc5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Cbln1 C1q domain trimer | ||||||
![]() | Cerebellin-1 | ||||||
![]() | SIGNALING PROTEIN / Cerebellin / C1q / neurotransmission | ||||||
Function / homology | ![]() negative regulation of inhibitory 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 / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of presynapse assembly ...negative regulation of inhibitory 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 / positive regulation of synapse assembly / parallel fiber to Purkinje cell synapse / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of presynapse assembly / protein secretion / synaptic cleft / synapse assembly / establishment of localization in cell / synapse organization / nervous system development / chemical synaptic transmission / postsynaptic membrane / collagen-containing extracellular matrix / glutamatergic synapse / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elegheert, J. / Clay, J.E. / Siebold, C. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 43.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 28.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 422.1 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 6.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5kc6C ![]() 5kc7C ![]() 5kc8C ![]() 5kc9C ![]() 5kcaC ![]() 1gr3S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Symmetry | Point symmetry: (Schoenflies symbol: C3 (3 fold cyclic)) |
-
Components
#1: Protein | Mass: 16642.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.71 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium malonate pH 7.0, 20% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.073 Å / Relative weight: 1 |
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.17 |
Reflection | Resolution: 2.35→50.57 Å / Num. obs: 8497 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 40.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.126 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.263 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1GR3 Resolution: 2.351→50.55 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.81 / Stereochemistry target values: TWIN_LSQ_F Details: Refined with twin operator h, -h-k, -l to account for higher P622 metric symmetry
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.351→50.55 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|