+Open data
-Basic information
Entry | Database: PDB / ID: 3wsx | ||||||
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Title | SorLA Vps10p domain in ligand-free form | ||||||
Components | Sortilin-related receptor | ||||||
Keywords | PROTEIN BINDING / Beta-Propeller / Receptor | ||||||
Function / homology | Function and homology information positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / adaptive thermogenesis / post-Golgi vesicle-mediated transport / protein retention in Golgi apparatus ...positive regulation of early endosome to recycling endosome transport / negative regulation of neurofibrillary tangle assembly / positive regulation of glial cell-derived neurotrophic factor production / perinucleolar compartment / positive regulation of endocytic recycling / Golgi cisterna / positive regulation of ER to Golgi vesicle-mediated transport / adaptive thermogenesis / post-Golgi vesicle-mediated transport / protein retention in Golgi apparatus / endosome to plasma membrane protein transport / low-density lipoprotein particle receptor activity / negative regulation of triglyceride catabolic process / protein localization to Golgi apparatus / positive regulation of protein localization to early endosome / low-density lipoprotein particle binding / positive regulation of protein exit from endoplasmic reticulum / negative regulation of amyloid precursor protein catabolic process / protein targeting to lysosome / multivesicular body membrane / neuropeptide binding / aspartic-type endopeptidase inhibitor activity / regulation of smooth muscle cell migration / transport vesicle membrane / insulin receptor recycling / nuclear envelope lumen / diet induced thermogenesis / negative regulation of amyloid-beta formation / protein maturation / negative regulation of BMP signaling pathway / neuropeptide signaling pathway / protein targeting / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / positive regulation of adipose tissue development / multivesicular body / receptor-mediated endocytosis / trans-Golgi network / recycling endosome / small GTPase binding / negative regulation of neurogenesis / recycling endosome membrane / positive regulation of protein catabolic process / transmembrane signaling receptor activity / cell migration / amyloid-beta binding / early endosome membrane / early endosome / endosome membrane / endosome / Amyloid fiber formation / Golgi membrane / neuronal cell body / endoplasmic reticulum membrane / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Kitago, Y. / Nakata, Z. / Nagae, M. / Nogi, T. / Takagi, J. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2015 Title: Structural basis for amyloidogenic peptide recognition by sorLA. Authors: Kitago, Y. / Nagae, M. / Nakata, Z. / Yagi-Utsumi, M. / Takagi-Niidome, S. / Mihara, E. / Nogi, T. / Kato, K. / Takagi, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wsx.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wsx.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/3wsx ftp://data.pdbj.org/pub/pdb/validation_reports/ws/3wsx | HTTPS FTP |
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-Related structure data
Related structure data | 3wsyC 3wszC 3f6kS 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: 82839.961 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 29-753 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SORL1 / Plasmid: pEF / Cell line (production host): CHO Cells / Production host: Cricetulus Griseus (Chinese hamster) / Variant (production host): lec 3.2.8.1 / References: UniProt: Q92673 | ||||||
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#2: Sugar | #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-EDO / #5: 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: 4.04 Å3/Da / Density % sol: 69.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M Sodium Acetate, 1.2M Sodium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 8, 2010 Details: The double crystal monochromator and the K-B mirror system |
Radiation | Monochromator: Double Si 111 crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 57640 / Num. obs: 56199 / % possible obs: 97.5 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 11.4 % / Biso Wilson estimate: 56.6 Å2 / Rsym value: 0.057 / Net I/σ(I): 34 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.37 / Num. unique all: 5658 / Rsym value: 0.486 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F6K Resolution: 2.35→47.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.525 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R: 0.196 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 48.109 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→47.63 Å
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