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Yorodumi- PDB-1btg: CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1btg | ||||||
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Title | CRYSTAL STRUCTURE OF BETA NERVE GROWTH FACTOR AT 2.5 A RESOLUTION IN C2 SPACE GROUP WITH ZN IONS BOUND | ||||||
Components | BETA NERVE GROWTH FACTOR | ||||||
Keywords | GROWTH FACTOR / NERVE | ||||||
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 / metalloendopeptidase inhibitor activity / positive regulation of neuron maturation / 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 / positive regulation of DNA binding / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of stem cell proliferation / positive regulation of axon extension / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of protein autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / sensory perception of pain / 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 / memory / positive regulation of neuron projection development / circadian rhythm / neuron projection development / 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 / endoplasmic reticulum lumen / axon / lipid binding / dendrite / 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 / Resolution: 2.5 Å | ||||||
Authors | Holland, D.R. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: Nerve growth factor in different crystal forms displays structural flexibility and reveals zinc binding sites. Authors: Holland, D.R. / Cousens, L.S. / Meng, W. / Matthews, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1btg.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1btg.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 1btg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/1btg ftp://data.pdbj.org/pub/pdb/validation_reports/bt/1btg | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 12382.035 Da / Num. of mol.: 3 Mutation: BIS-DES-OCTA (MISSING RESIDUES 1-8, PROTEOLYTICALLY CLEAVED) Source method: isolated from a genetically manipulated source Details: ZN IONS BOUND / Source: (gene. exp.) Mus musculus (house mouse) / Organ: SALIVARY GLANDS / References: UniProt: P01139 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64.07 % | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 63 % | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.1 / Method: vapor diffusion / Details: seeding | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Ambient pressure: 101 kPa / Mean temperature: 298 K |
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Diffraction source | Source: rotating-anode X-ray tube / Type: RIGAKU RU200 / Wavelength: 1.54 / Target: Cu |
Detector | Type: AREA DETECTOR / Detector: AREA DETECTOR / Date: Jan 1, 1993 / Details: Xuong-Hamlin |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5418 Å |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Rmerge(I) obs: 0.05 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 15194 / % possible obs: 89 % / Num. measured all: 44269 / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / σ(F): 2 Details: ALTHOUGH THE N- AND C-TERMINI OF THE A, B, AND C MOLECULES ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS, THEY ARE SEEN IN OMIT MAPS.
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 15194 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |