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- PDB-2ifg: Structure of the extracellular segment of human TRKA in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ifg | |||||||||
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Title | Structure of the extracellular segment of human TRKA in complex with nerve growth factor | |||||||||
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![]() | TRANSFERASE / TRK / TRKA / NGF / NERVE GROWTH FACTOR / RECEPTOR-LIGAND COMPLEX | |||||||||
Function / homology | ![]() NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling ...NFG and proNGF binds to p75NTR / Ceramide signalling / nerve growth factor receptor binding / NGF processing / behavioral response to formalin induced pain / neurotrophin p75 receptor binding / olfactory nerve development / response to hydrostatic pressure / TRKA activation by NGF / PLC-gamma1 signalling / programmed cell death involved in cell development / Signalling to STAT3 / p75NTR negatively regulates cell cycle via SC1 / neurotrophin receptor activity / mechanoreceptor differentiation / nerve growth factor receptor activity / metalloendopeptidase inhibitor activity / neurotrophin binding / Sertoli cell development / axonogenesis involved in innervation / GPI-linked ephrin receptor activity / nerve growth factor signaling pathway / nerve development / Retrograde neurotrophin signalling / Axonal growth stimulation / positive regulation of collateral sprouting / nerve growth factor binding / NGF-independant TRKA activation / NADE modulates death signalling / sympathetic nervous system development / Signalling to p38 via RIT and RIN / peripheral nervous system development / ARMS-mediated activation / positive regulation of Ras protein signal transduction / positive regulation of programmed cell death / positive regulation of synapse assembly / PI3K/AKT activation / regulation of neuron differentiation / Frs2-mediated activation / NRAGE signals death through JNK / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / detection of temperature stimulus involved in sensory perception of pain / neurotrophin TRK receptor signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / response to axon injury / neuron development / Signalling to RAS / positive regulation of DNA binding / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / p75NTR recruits signalling complexes / positive regulation of neuron differentiation / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / transmembrane receptor protein tyrosine kinase activity / positive regulation of synaptic transmission, glutamatergic / response to nutrient levels / B cell differentiation / neuron projection morphogenesis / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / endosome lumen / axon guidance / growth factor activity / modulation of chemical synaptic transmission / receptor protein-tyrosine kinase / memory / kinase binding / positive regulation of neuron projection development / Golgi lumen / cellular response to nicotine / circadian rhythm / peptidyl-tyrosine phosphorylation / recycling endosome membrane / positive regulation of angiogenesis / neuron projection development / synaptic vesicle / late endosome / positive regulation of peptidyl-serine phosphorylation / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / early endosome membrane / protein tyrosine kinase activity / neuron apoptotic process / negative regulation of neuron apoptotic process / protein autophosphorylation / learning or memory / positive regulation of ERK1 and ERK2 cascade / early endosome / receptor complex / endosome membrane / response to xenobiotic stimulus / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / axon / protein phosphorylation / neuronal cell body / lipid binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | He, X. / Garcia, K.C. | |||||||||
![]() | ![]() Title: Structural and mechanistic insights into nerve growth factor interactions with the TrkA and p75 receptors. Authors: Wehrman, T. / He, X. / Raab, B. / Dukipatti, A. / Blau, H. / 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 | ![]() | 191.2 KB | Display | ![]() |
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PDB format | ![]() | 154.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.3 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 43.5 KB | Display | |
Data in CIF | ![]() | 58.4 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: 37898.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04629, receptor protein-tyrosine kinase #2: Protein | Mass: 13515.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.91 Å3/Da / Density % sol: 75 % |
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Crystal grow | pH: 7.5 Details: PEG, GLYCINE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 26668 / % possible obs: 99 % / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.4→3.5 Å / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WWW Resolution: 3.4→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3.4→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.5 Å / Rfactor Rfree: 0.391 / Rfactor Rwork: 0.37 |