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Open data
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Basic information
Entry | Database: PDB / ID: 1hcf | ||||||
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Title | Crystal structure of TrkB-d5 bound to neurotrophin-4/5 | ||||||
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![]() | TRANSFERASE/HORMONE / COMPLEX(TRANSFERASE-GROWTH FACTOR) / NEUROTROPHIN-4/5 / TRKB RECEPTOR / NGF-BETA SUPERFAMILY / IMMUNOGLOBULIN DOMAIN / TRANSFERASE-HORMONE complex | ||||||
Function / homology | ![]() taste bud development / sensory organ boundary specification / brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / ganglion mother cell fate determination / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 ...taste bud development / sensory organ boundary specification / brain-derived neurotrophic factor receptor activity / trans-synaptic signaling by neuropeptide, modulating synaptic transmission / ganglion mother cell fate determination / BDNF activates NTRK2 (TRKB) signaling / NTF4 activates NTRK2 (TRKB) signaling / NTF3 activates NTRK2 (TRKB) signaling / brain-derived neurotrophic factor receptor signaling pathway / Activated NTRK2 signals through PLCG1 / retinal rod cell development / peripheral nervous system neuron development / nerve growth factor receptor binding / brain-derived neurotrophic factor binding / trans-synaptic signaling by BDNF, modulating synaptic transmission / mechanoreceptor differentiation / neurotrophin binding / Activated NTRK2 signals through CDK5 / nerve growth factor signaling pathway / NTRK2 activates RAC1 / Activated NTRK2 signals through FYN / nerve development / NGF-independant TRKA activation / myelination in peripheral nervous system / innervation / peripheral nervous system development / Activated NTRK2 signals through PI3K / glutamate secretion / feeding behavior / neuronal action potential propagation / positive regulation of synapse assembly / regulation of neuron differentiation / positive regulation of axonogenesis / regulation of GTPase activity / central nervous system neuron development / oligodendrocyte differentiation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of amyloid-beta formation / negative regulation of anoikis / Activated NTRK2 signals through RAS / epidermis development / vasculogenesis / Activated NTRK2 signals through FRS2 and FRS3 / long-term memory / axon terminus / cellular response to brain-derived neurotrophic factor stimulus / cell surface receptor protein tyrosine kinase signaling pathway / adult locomotory behavior / neuron projection morphogenesis / learning / long-term synaptic potentiation / cellular response to amino acid stimulus / growth factor activity / neuron migration / modulation of chemical synaptic transmission / neuron differentiation / terminal bouton / receptor protein-tyrosine kinase / cerebral cortex development / memory / positive regulation of neuron projection development / circadian rhythm / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / early endosome membrane / protease binding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / protein autophosphorylation / dendritic spine / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / receptor complex / positive regulation of protein phosphorylation / axon / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Banfield, M.J. / Naylor, R.L. / Robertson, A.G.S. / Allen, S.J. / Dawbarn, D. / Brady, R.L. | ||||||
![]() | ![]() Title: Specificity in Trk-Receptor:Neurotrophin Interaction: The Crystal Structure of Trkb-D5 in Complex with Neurotrophin-4/5 Authors: Banfield, M.J. / Naylor, R.L. / Robertson, A.G.S. / Allen, S.J. / Dawbarn, D. / Brady, R.L. #1: ![]() Title: Identification and Structure of the Nerve Growth Factor Binding Site on Trka Authors: Robertson, A.G.S. / Banfield, M.J. / Allen, S.J. / Dando, J.A. / Mason, G.G.F. / Tyler, S.J. / Bennett, G.S. / Brain, S.D. / Clarke, A.R. / Brady, R.L. / Dawbarn, D. #2: ![]() Title: Crystal Structure of Nerve Growth Factor in Complex with the Ligand-Binding Domain of the Trka Receptor Authors: Wiesmann, C. / Ultsch, M.H. / Bass, S.H. / Devos, A.M. #3: ![]() Title: Crystal Structures of the Neurotrophin Binding Domain of Trka, Trkb and Trkc Authors: Ultsch, M.H. / Wiesmann, C. / Simmons, L.C. / Henrich, J. / Yang, M. / Reilly, D. / Bass, S.H. / Devos, A.M. #4: ![]() Title: The Structures of 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. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.6 KB | Display | ![]() |
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PDB format | ![]() | 76.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.3 KB | Display | ![]() |
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Full document | ![]() | 476.5 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | COMPLEX OF HOMODIMERIC NEUROTROPHIN-4 AND TWO CHAINSOF TRKB |
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Components
#1: Protein | Mass: 13944.647 Da / Num. of mol.: 2 / Fragment: ACTIVE, FRAGMENT. PRO-REGION CLEAVED / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 11545.979 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN 5 (RESIDUES 286 - 383) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | RESIDUES NUMBERED X283, X284, X285 ARE CLONING ARTEFACTS. THEY ARE DERIVED FROM THE HIS-TAG ...RESIDUES NUMBERED X283, X284, X285 ARE CLONING ARTEFACTS. THEY ARE DERIVED FROM THE HIS-TAG SEQUENCE OF THE PET-15B PLASMID, AND DO NOT CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 46.6 % | ||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 10 MG/ML COMPLEX IN 20MM TRIS, 150MM NACL, PH 7.5, 100MM HEPES PH 7.5, 1.5M LISO4 | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / PH range low: 7.5 / PH range high: 7 | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 15635 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 63.7 Å2 / Rsym value: 0.084 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.294 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.294 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1B98 (NEUROTROPHIN), 1WWB (TRK) Resolution: 2.7→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.14 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.299 |