+Open data
-Basic information
Entry | Database: PDB / ID: 6ffy | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the mouse SorCS2-NGF complex | |||||||||
Components |
| |||||||||
Keywords | APOPTOSIS / SorCS2 / proNGF / p75NTR / VPS10 / Sortilin / neuroplasticity | |||||||||
Function / homology | Function and homology information TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation ...TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / Axonal growth stimulation / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process / positive regulation of neurotrophin TRK receptor signaling pathway / PI3K/AKT activation / ARMS-mediated activation / nerve growth factor receptor binding / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / Retrograde neurotrophin signalling / NF-kB is activated and signals survival / positive regulation of neuron maturation / death receptor agonist activity / metalloendopeptidase inhibitor activity / nerve growth factor signaling pathway / regulation of neurotransmitter secretion / nerve development / positive regulation of collateral sprouting / peripheral nervous system development / regulation of release of sequestered calcium ion into cytosol / axon extension / positive regulation of Ras protein signal transduction / long-term synaptic depression / regulation of neuron differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of stem cell proliferation / cysteine-type endopeptidase activator activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of axon extension / positive regulation of DNA binding / sensory perception of pain / positive regulation of protein autophosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of neuron differentiation / adult locomotory behavior / neuron projection morphogenesis / positive regulation of protein ubiquitination / endosome lumen / postsynaptic density membrane / intracellular protein transport / growth factor activity / modulation of chemical synaptic transmission / positive regulation of neuron projection development / memory / circadian rhythm / recycling endosome membrane / neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / perikaryon / early endosome membrane / positive regulation of cell growth / neuron apoptotic process / negative regulation of neuron apoptotic process / dendritic spine / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / axon / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / dendrite / lipid binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | |||||||||
Authors | Leloup, N.O.L. / Janssen, B.J.C. | |||||||||
Funding support | Netherlands, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ffy.cif.gz | 244.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ffy.ent.gz | 190.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ffy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/6ffy ftp://data.pdbj.org/pub/pdb/validation_reports/ff/6ffy | HTTPS FTP |
---|
-Related structure data
Related structure data | 6fg9C 1wgoS 4aqoS 4eaxS 4mslS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 109115.305 Da / Num. of mol.: 1 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: Protein | Mass: 14361.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngf, Ngfb / Production host: Homo sapiens (human) / References: UniProt: P01139 #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.94 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.225 M MES/bis-tris pH 6.6 and 6.6 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99998 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→61 Å / Num. obs: 25900 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.34 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 3.6→3.85 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4621 / CC1/2: 0.178 / % possible all: 99.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EAX,4MSL,1WGO,4AQO Resolution: 3.9→60.841 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.18 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→60.841 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|