+Open data
-Basic information
Entry | Database: PDB / ID: 5h48 | |||||||||
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Title | Crystal structure of Cbln1 | |||||||||
Components | Cerebellin-1 | |||||||||
Keywords | PROTEIN BINDING / C1q domain / C1q/TNF superfamily / receptor specificity / synaptogenesis | |||||||||
Function / homology | Function and homology information 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 / postsynaptic membrane / glutamatergic synapse / synapse / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Zhong, C. / Shen, J. / Zhang, H. / Ding, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell Rep / Year: 2017 Title: Cbln1 and Cbln4 Are Structurally Similar but Differ in GluD2 Binding Interactions. Authors: Chen Zhong / Jinlong Shen / Huibing Zhang / Guangyi Li / Senlin Shen / Fang Wang / Kuan Hu / Longxing Cao / Yongning He / Jianping Ding / Abstract: Unlike cerebellin 1 (Cbln1), which bridges neurexin (Nrxn) receptors and δ-type glutamate receptors in a trans-synaptic triad, Cbln4 was reported to have no or weak binding for the receptors ...Unlike cerebellin 1 (Cbln1), which bridges neurexin (Nrxn) receptors and δ-type glutamate receptors in a trans-synaptic triad, Cbln4 was reported to have no or weak binding for the receptors despite sharing ∼70% sequence identity with Cbln1. Here, we report crystal structures of the homotrimers of the C1q domain of Cbln1 and Cbln4 at 2.2 and 2.3 Å resolution, respectively. Comparison of the structures suggests that the difference between Cbln1 and Cbln4 in GluD2 binding might be because of their sequence and structural divergence in loop CD. Surprisingly, we show that Cbln4 binds to Nrxn1β and forms a stable complex with the laminin, nectin, sex-hormone binding globulin (LNS) domain of Nrxn1β. Furthermore, the negative-stain electron microscopy reconstruction of hexameric full-length Cbln1 at 13 Å resolution and that of the Cbln4/Nrxn1β complex at 19 Å resolution suggest that Nrxn1β binds to the N-terminal region of Cbln4, probably through strand β10 of the S4 insert. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h48.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h48.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 5h48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/5h48 ftp://data.pdbj.org/pub/pdb/validation_reports/h4/5h48 | HTTPS FTP |
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-Related structure data
Related structure data | 6665C 6666C 5h49C 5h4bC 5h4cC 4nn0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20418.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cbln1 / Production host: Homo sapiens (human) / References: UniProt: P63182 |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.2 M Sodium tartrate dibasic dihydrate, 20% PEG3350, pH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9199 Å |
Detector | Type: RAYONIX MX-325 / Detector: CCD / Date: Oct 31, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→71.86 Å / Num. obs: 9670 / % possible obs: 94.7 % / Redundancy: 3.9 % / Net I/σ(I): 13.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NN0 Resolution: 2.2→71.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.473 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.338 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→71.86 Å
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