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- PDB-1sg1: Crystal Structure of the Receptor-Ligand Complex between Nerve Gr... -
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Basic information
Entry | Database: PDB / ID: 1sg1 | ||||||
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Title | Crystal Structure of the Receptor-Ligand Complex between Nerve Growth Factor and the Common Neurotrophin Receptor p75 | ||||||
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![]() | HORMONE/GROWTH FACTOR/MEMBRANE PROTEIN / Nerve Growth Factor / NGF / p75 / Neurotrophin / common neurotrophin receptor / growth factor receptor / receptor-ligand complex / HORMONE-GROWTH FACTOR-MEMBRANE PROTEIN COMPLEX | ||||||
Function / homology | ![]() Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NFG and proNGF binds to p75NTR / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development ...Regulated proteolysis of p75NTR / NFG and proNGF binds to p75NTR / NADE modulates death signalling / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / NFG and proNGF binds to p75NTR / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / detection of temperature stimulus / dorsal aorta development / p75NTR recruits signalling complexes / Ceramide signalling / death receptor activity / nerve growth factor receptor binding / preprotein binding / positive regulation of odontogenesis of dentin-containing tooth / negative regulation of hair follicle development / NGF processing / positive regulation of synaptic transmission, cholinergic / TRKA activation by NGF / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / PLC-gamma1 signalling / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / negative regulation of dendritic spine development / metalloendopeptidase inhibitor activity / neurotrophin binding / positive regulation of myelination / nerve growth factor signaling pathway / nerve development / Retrograde neurotrophin signalling / Axonal growth stimulation / positive regulation of collateral sprouting / clathrin-coated endocytic vesicle / nerve growth factor binding / NADE modulates death signalling / Signalling to p38 via RIT and RIN / peripheral nervous system development / neurotrophin TRKA receptor binding / ARMS-mediated activation / positive regulation of neural precursor cell proliferation / positive regulation of Ras protein signal transduction / regulation of reactive oxygen species metabolic process / negative regulation of mitochondrial depolarization / PI3K/AKT activation / regulation of neuron differentiation / skin development / hair follicle morphogenesis / Frs2-mediated activation / positive regulation of Rho protein signal transduction / neuronal cell body membrane / NRAGE signals death through JNK / skeletal muscle cell differentiation / intracellular glucose homeostasis / odontogenesis of dentin-containing tooth / positive regulation of excitatory postsynaptic potential / Rho protein signal transduction / extrinsic apoptotic signaling pathway via death domain receptors / hair follicle development / Signalling to RAS / fibroblast growth factor receptor signaling pathway / positive regulation of DNA binding / coreceptor activity / dendrite membrane / cell surface receptor protein tyrosine kinase signaling pathway / p75NTR recruits signalling complexes / presynaptic modulation of chemical synaptic transmission / positive regulation of neuron differentiation / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / negative regulation of angiogenesis / negative regulation of cell migration / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / central nervous system development / endosome lumen / positive regulation of apoptotic signaling pathway / axon guidance / intracellular protein transport / growth factor activity / circadian regulation of gene expression / modulation of chemical synaptic transmission / neuromuscular junction / memory / small GTPase binding / positive regulation of neuron projection development / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / Golgi lumen / circadian rhythm / cellular response to amyloid-beta / positive regulation of fibroblast proliferation / cell-cell junction / synaptic vesicle / presynapse / positive regulation of peptidyl-serine phosphorylation / negative regulation of neuron projection development / glucose homeostasis / nuclear envelope Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | He, X.L. / Garcia, K.C. | ||||||
![]() | ![]() Title: Structure of nerve growth factor complexed with the shared neurotrophin receptor p75 Authors: He, X.L. / Garcia, K.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.5 KB | Display | ![]() |
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PDB format | ![]() | 69.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.8 KB | Display | ![]() |
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Full document | ![]() | 462.2 KB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wwwS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13515.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 17258.014 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: PEG 1000, isoproponal, sodium chloride, citrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2003 / Details: null |
Radiation | Monochromator: null / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0597 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 16891 / Num. obs: 16891 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.4 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: part of the structure starts from PDB ENTRY 1WWW Resolution: 2.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 50.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å
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