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Open data
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Basic information
Entry | Database: PDB / ID: 1b8m | ||||||
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Title | BRAIN DERIVED NEUROTROPHIC FACTOR, NEUROTROPHIN-4 | ||||||
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![]() | GROWTH FACTOR/NEUROTROPHIN-4 / COMPLEX (GROWTH FACTOR-GROWTH FACTOR) / NEUROTROPHIN / GROWTH FACTOR-NEUROTROPHIN-4 COMPLEX | ||||||
Function / homology | ![]() taste bud development / positive regulation of brain-derived neurotrophic factor receptor signaling pathway / sensory organ boundary specification / ganglion mother cell fate determination / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands ...taste bud development / positive regulation of brain-derived neurotrophic factor receptor signaling pathway / sensory organ boundary specification / ganglion mother cell fate determination / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / nerve growth factor receptor binding / MECP2 regulates transcription of neuronal ligands / mechanoreceptor differentiation / negative regulation of myotube differentiation / Activated NTRK2 signals through CDK5 / nerve growth factor signaling pathway / NTRK2 activates RAC1 / collateral sprouting / Activated NTRK2 signals through FYN / regulation of protein localization to cell surface / nerve development / positive regulation of collateral sprouting / innervation / peripheral nervous system development / Activated NTRK2 signals through PI3K / positive regulation of synapse assembly / regulation of neuron differentiation / negative regulation of apoptotic signaling pathway / Activated NTRK2 signals through RAS / epidermis development / Activated NTRK2 signals through FRS2 and FRS3 / long-term memory / cell surface receptor protein tyrosine kinase signaling pathway / synapse assembly / NPAS4 regulates expression of target genes / adult locomotory behavior / neuron projection morphogenesis / positive regulation of receptor binding / axon guidance / growth factor activity / modulation of chemical synaptic transmission / memory / positive regulation of neuron projection development / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / nervous system development / negative regulation of neuron apoptotic process / endoplasmic reticulum lumen / axon / dendrite / perinuclear region of cytoplasm / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Robinson, R.C. / Radziejewski, C. / Stuart, D.I. / Jones, E.Y. / Choe, S. | ||||||
![]() | ![]() Title: The structures of the neurotrophin 4 homodimer and the brain-derived neurotrophic factor/neurotrophin 4 heterodimer reveal a common Trk-binding site. Authors: Robinson, R.C. / Radziejewski, C. / Spraggon, G. / Greenwald, J. / Kostura, M.R. / Burtnick, L.D. / Stuart, D.I. / Choe, S. / Jones, E.Y. #1: ![]() Title: Structure of the Brain-Derived Neurotrophic Factor (Slash)Neurotrophin 3 Heterodimer Authors: Robinson, R.C. / Radziejewski, C. / Stuart, D.I. / Jones, E.Y. #2: ![]() Title: Heterodimers of the Neurotrophic Factors: Formation, Isolation, and Differential Stability Authors: Radziejewski, C. / Robinson, R.C. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.7 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 374.8 KB | Display | ![]() |
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Full document | ![]() | 377.7 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b8kC ![]() 1b98C ![]() 1bnfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13535.575 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 13944.647 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 50 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 270 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→20 Å / Num. obs: 7858 / % possible obs: 98 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BNF Resolution: 2.75→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 36.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→20 Å
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Refine LS restraints |
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