+Open data
-Basic information
Entry | Database: PDB / ID: 3wsy | ||||||
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Title | SorLA Vps10p domain in complex with its own propeptide fragment | ||||||
Components |
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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 / post-Golgi vesicle-mediated transport / adaptive thermogenesis / 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 / post-Golgi vesicle-mediated transport / adaptive thermogenesis / protein retention in Golgi apparatus / low-density lipoprotein particle receptor activity / negative regulation of triglyceride catabolic process / protein localization to Golgi apparatus / endosome to plasma membrane protein transport / 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 / aspartic-type endopeptidase inhibitor activity / multivesicular body membrane / neuropeptide binding / regulation of smooth muscle cell migration / negative regulation of BMP signaling pathway / transport vesicle membrane / insulin receptor recycling / nuclear envelope lumen / diet induced thermogenesis / negative regulation of amyloid-beta formation / protein maturation / neuropeptide signaling pathway / positive regulation of adipose tissue development / protein targeting / negative regulation of protein-containing complex assembly / positive regulation of insulin receptor signaling pathway / multivesicular body / receptor-mediated endocytosis / trans-Golgi network / recycling endosome / transmembrane signaling receptor activity / small GTPase binding / negative regulation of neurogenesis / positive regulation of protein catabolic process / recycling endosome membrane / cell migration / early endosome membrane / amyloid-beta binding / endosome / endosome membrane / early endosome / Amyloid fiber formation / Golgi membrane / neuronal cell body / endoplasmic reticulum membrane / cell surface / Golgi apparatus / 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: 3.11 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 | 3wsy.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wsy.ent.gz | 115.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wsy_validation.pdf.gz | 466.5 KB | Display | wwPDB validaton report |
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Full document | 3wsy_full_validation.pdf.gz | 484.4 KB | Display | |
Data in XML | 3wsy_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 3wsy_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/3wsy ftp://data.pdbj.org/pub/pdb/validation_reports/ws/3wsy | HTTPS FTP |
-Related structure data
Related structure data | 3wsxSC 3wszC S: Starting model for refinement C: citing same article (ref.) |
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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: 76568.766 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 86-753 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: Protein/peptide | Mass: 1698.920 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: This sequence exists at the upstream of Sortilin-related receptor Source: (synth.) Homo sapiens (human) / References: UniProt: Q92673 | ||
#3: Sugar | ChemComp-NAG / Sequence details | THIS RESIDUE BELONGS TO PROTEIN SEQUENCE, 29TH GLU OF Q92673. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.82 Å3/Da / Density % sol: 78.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Cacodylate, 1.2M Sodium Acetate, pH 6.5, 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 315r / Detector: CCD / Date: Feb 26, 2011 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: 3.1→50.02 Å / Num. all: 31939 / Num. obs: 31428 / % possible obs: 98.4 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 4.3 % / Biso Wilson estimate: 66.7 Å2 / Rsym value: 0.07 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.31 / Num. unique all: 3182 / Rsym value: 0.51 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WSX Resolution: 3.11→50.02 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / SU B: 12.825 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.555 / ESU R Free: 0.325 / 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: 60.635 Å2
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Refinement step | Cycle: LAST / Resolution: 3.11→50.02 Å
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