+Open data
-Basic information
Entry | Database: PDB / ID: 4eax | ||||||
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Title | Mouse NGF in complex with Lyso-PS | ||||||
Components | Beta-nerve growth factor | ||||||
Keywords | HORMONE / Lyso-PS / phospholipid | ||||||
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 / 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 / growth factor activity / modulation of chemical synaptic transmission / positive regulation of neuron projection development / memory / circadian rhythm / neuron projection development / cell surface receptor protein tyrosine kinase signaling pathway / synaptic vesicle / positive regulation of peptidyl-serine phosphorylation / positive regulation of cell growth / neuron apoptotic process / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / axon / endoplasmic reticulum lumen / dendrite / lipid binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Jiang, T. / Tong, Q. | ||||||
Citation | Journal: Faseb J. / Year: 2012 Title: Structural and functional insights into lipid-bound nerve growth factors Authors: Tong, Q. / Wang, F. / Zhou, H.Z. / Sun, H.L. / Song, H. / Shu, Y.Y. / Gong, Y. / Zhang, W.T. / Cai, T.X. / Yang, F.Q. / Tang, J. / Jiang, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eax.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eax.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 4eax.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/4eax ftp://data.pdbj.org/pub/pdb/validation_reports/ea/4eax | HTTPS FTP |
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-Related structure data
Related structure data | 4ec7C 1btgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13491.255 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01139 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.8 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Imidazole, 1.0M Sodium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.3→40.5 Å / Num. all: 25278 / Num. obs: 24969 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 46.03 Å2 | ||||||||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2240 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BTG Resolution: 2.3→40.5 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7797 / SU ML: 0.33 / σ(F): 0.13 / Phase error: 29.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.217 Å2 / ksol: 0.391 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.72 Å2 / Biso mean: 58.4532 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
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