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Yorodumi- PDB-6fg9: Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fg9 | ||||||
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Title | Mouse SORCS2 ectodomain (sortilin related VPS10 domain containing receptor 2) | ||||||
Components | VPS10 domain-containing receptor SorCS2 | ||||||
Keywords | APOPTOSIS / SorCS2 / VPS10 / transport / sorting / Sortilin | ||||||
Function / homology | Function and homology information long-term synaptic depression / intracellular protein transport / postsynaptic density membrane / recycling endosome membrane / early endosome membrane / perikaryon / dendritic spine / postsynaptic density / intracellular membrane-bounded organelle / membrane ...long-term synaptic depression / intracellular protein transport / postsynaptic density membrane / recycling endosome membrane / early endosome membrane / perikaryon / dendritic spine / postsynaptic density / intracellular membrane-bounded organelle / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å | ||||||
Authors | Leloup, N.O.L. / Janssen, B.J.C. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural insights into SorCS2-Nerve Growth Factor complex formation. Authors: Leloup, N. / Chataigner, L.M.P. / Janssen, B.J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fg9.cif.gz | 383.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fg9.ent.gz | 303.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fg9_validation.pdf.gz | 470.9 KB | Display | wwPDB validaton report |
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Full document | 6fg9_full_validation.pdf.gz | 485.1 KB | Display | |
Data in XML | 6fg9_validation.xml.gz | 62.4 KB | Display | |
Data in CIF | 6fg9_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/6fg9 ftp://data.pdbj.org/pub/pdb/validation_reports/fg/6fg9 | HTTPS FTP |
-Related structure data
Related structure data | 6ffyC 1wgoS 4aqoS 4smlS 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: 109115.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sorcs2 / Production host: Homo sapiens (human) / References: UniProt: Q9EPR5 #2: 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: 3.44 Å3/Da / Density % sol: 64.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.1 M Sodium chloride, 0.02 M Tris pH 7.5, 0.1 M Magnesium chloride hexahydrate and 11 % w/v PEG 1500, final pH 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 4→49.203 Å / Num. obs: 26077 / % possible obs: 99.8 % / Redundancy: 6.4 % / CC1/2: 1 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5 |
Reflection shell | Resolution: 4→4.26 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4652 / CC1/2: 0.35 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4SML, 1WGO, 4AQO Resolution: 4.2→49.203 Å / SU ML: 0.67 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.2→49.203 Å
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Refine LS restraints |
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LS refinement shell |
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