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Yorodumi- PDB-5b4x: Crystal structure of the ApoER2 ectodomain in complex with the Re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b4x | |||||||||||||||
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Title | Crystal structure of the ApoER2 ectodomain in complex with the Reelin R56 fragment | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN/ENDOCYTOSIS / signal transduction / MEMBRANE PROTEIN / SIGNALING PROTEIN-ENDOCYTOSIS complex | |||||||||||||||
Function / homology | Function and homology information ammon gyrus development / spinal cord patterning / cerebral cortex tangential migration / reelin complex / positive regulation of lateral motor column neuron migration / lateral motor column neuron migration / Reelin signalling pathway / lipoprotein particle receptor binding / reelin receptor activity / regulation of synaptic activity ...ammon gyrus development / spinal cord patterning / cerebral cortex tangential migration / reelin complex / positive regulation of lateral motor column neuron migration / lateral motor column neuron migration / Reelin signalling pathway / lipoprotein particle receptor binding / reelin receptor activity / regulation of synaptic activity / interneuron migration / postsynaptic density protein 95 clustering / positive regulation of CREB transcription factor activity / postsynaptic density assembly / ventral spinal cord development / very-low-density lipoprotein particle receptor activity / regulation of behavior / reelin-mediated signaling pathway / high-density lipoprotein particle binding / positive regulation of synapse maturation / low-density lipoprotein particle receptor activity / motor neuron migration / layer formation in cerebral cortex / receptor localization to synapse / glial cell differentiation / regulation of neuron migration / cellular response to cholesterol / protein localization to synapse / NMDA glutamate receptor clustering / positive regulation of dendritic spine morphogenesis / regulation of synapse maturation / very-low-density lipoprotein particle receptor binding / dentate gyrus development / positive regulation of small GTPase mediated signal transduction / positive regulation of AMPA receptor activity / regulation of NMDA receptor activity / positive regulation of dendrite development / dendrite morphogenesis / cargo receptor activity / microtubule associated complex / retinoid metabolic process / regulation of neuron differentiation / Platelet sensitization by LDL / response to pain / regulation of innate immune response / dendrite development / kinesin binding / associative learning / positive regulation of excitatory postsynaptic potential / apolipoprotein binding / positive regulation of protein tyrosine kinase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of TOR signaling / long-term memory / positive regulation of synaptic transmission, glutamatergic / Retinoid metabolism and transport / forebrain development / serine-type peptidase activity / extracellular matrix / learning / positive regulation of long-term synaptic potentiation / caveola / central nervous system development / axon guidance / locomotory behavior / hippocampus development / lipid metabolic process / long-term synaptic potentiation / neuron migration / modulation of chemical synaptic transmission / brain development / cell morphogenesis / transmembrane signaling receptor activity / cellular response to growth factor stimulus / cerebral cortex development / positive regulation of neuron projection development / cytokine-mediated signaling pathway / endocytosis / calcium-dependent protein binding / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / regulation of gene expression / amyloid-beta binding / chemical synaptic transmission / perikaryon / collagen-containing extracellular matrix / regulation of apoptotic process / receptor complex / membrane => GO:0016020 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / cell adhesion / positive regulation of protein phosphorylation / neuron projection / response to xenobiotic stimulus / axon / neuronal cell body / synapse / dendrite / calcium ion binding Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | |||||||||||||||
Authors | Yasui, N. / Hirai, H. / Yamashita, K. / Takagi, J. / Nogi, T. | |||||||||||||||
Funding support | Japan, 4items
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Citation | Journal: To Be Published Title: Crystal structure of the ectodomain from a LDLR close homologue in complex with its physiological ligand. Authors: Hirai, H. / Yasui, N. / Yamashita, K. / Tabata, S. / Yamamoto, M. / Takagi, J. / Nogi, T. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b4x.cif.gz | 488.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b4x.ent.gz | 391.4 KB | Display | PDB format |
PDBx/mmJSON format | 5b4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b4x_validation.pdf.gz | 496.5 KB | Display | wwPDB validaton report |
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Full document | 5b4x_full_validation.pdf.gz | 530.4 KB | Display | |
Data in XML | 5b4x_validation.xml.gz | 81.2 KB | Display | |
Data in CIF | 5b4x_validation.cif.gz | 109.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/5b4x ftp://data.pdbj.org/pub/pdb/validation_reports/b4/5b4x | HTTPS FTP |
-Related structure data
-Links
-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: 81786.039 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1948-2662 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Reln, Rl / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: Q60841, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein | Mass: 63649.109 Da / Num. of mol.: 2 / Fragment: ApoER2 ectodomain (UNP RESIDUES 42-607) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LRP8, hCG_33395 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: D3DQ39, UniProt: Q14114*PLUS #3: Chemical | ChemComp-CA / #4: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 11-12.5%(wt./vol.) PEG 3350 200-250mM sodium thiocyanate, 20mM HEPES-Na (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97904 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→49.52 Å / Num. obs: 67441 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 3.2→3.28 Å |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3.2→49.52 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.891 / SU B: 20.108 / SU ML: 0.342 / Cross valid method: FREE R-VALUE / ESU R Free: 0.451
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 99.77 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→49.52 Å
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