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Yorodumi- PDB-1sgf: CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WIT... -
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-Basic information
Entry | Database: PDB / ID: 1sgf | |||||||||
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Title | CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WITH FOUR BINDING PROTEINS (SERINE PROTEINASES) | |||||||||
Components | (NERVE GROWTH ...) x 3 | |||||||||
Keywords | GROWTH FACTOR / GROWTH FACTOR (BETA-NGF) / HYDROLASE - SERINE PROTEINASE (GAMMA-NGF) / INACTIVE SERINE PROTEINASE (ALPHA-NGF) | |||||||||
Function / homology | Function and homology information TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / tissue kallikrein / Axonal growth stimulation / Activation of Matrix Metalloproteinases / : / Frs2-mediated activation / negative regulation of type B pancreatic cell apoptotic process ...TRKA activation by NGF / NFG and proNGF binds to p75NTR / NADE modulates death signalling / NGF processing / tissue kallikrein / Axonal growth stimulation / Activation of Matrix Metalloproteinases / : / 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 / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / nerve growth factor signaling pathway / regulation of neurotransmitter secretion / nerve development / positive regulation of collateral sprouting / regulation of systemic arterial blood pressure / peripheral nervous system development / regulation of release of sequestered calcium ion into cytosol / axon extension / positive regulation of Ras protein signal transduction / zymogen activation / regulation of neuron differentiation / small GTPase-mediated signal transduction / 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 / secretory granule / 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 / endopeptidase activity / negative regulation of neuron apoptotic process / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / endoplasmic reticulum lumen / axon / serine-type endopeptidase activity / lipid binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / protein-containing complex / extracellular space / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | |||||||||
Authors | Bax, B.D.V. / Blundell, T.L. / Murray-Rust, J. / Mcdonald, N.Q. | |||||||||
Citation | Journal: Structure / Year: 1997 Title: Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins. Authors: Bax, B. / Blundell, T.L. / Murray-Rust, J. / McDonald, N.Q. #1: Journal: J.Mol.Biol. / Year: 1991 Title: Crystallization and Characterization of the High Molecular Weight Form of Nerve Growth Factor (7 S Ngf) Authors: Mcdonald, N.Q. / Blundell, T.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sgf.cif.gz | 203 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sgf.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 1sgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sg/1sgf ftp://data.pdbj.org/pub/pdb/validation_reports/sg/1sgf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9651, 0.25022, 0.07734), Vector: |
-Components
-NERVE GROWTH ... , 3 types, 6 molecules AXBYGZ
#1: Protein | Mass: 26783.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: MALE SUBMANDIBULAR GLAND / Strain: SWISS WEBSTER / References: UniProt: P00757, tissue kallikrein #2: Protein | Mass: 13277.009 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: MALE SUBMANDIBULAR GLAND / Strain: SWISS WEBSTER / References: UniProt: P01139, tissue kallikrein #3: Protein | Mass: 26432.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: MALE SUBMANDIBULAR GLAND / Strain: SWISS WEBSTER / References: UniProt: P00756, tissue kallikrein |
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-Sugars , 2 types, 4 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Non-polymers , 1 types, 2 molecules
#6: Chemical |
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-Details
Compound details | AN INTERNAL CLEAVAGE SITE EXISTS IN THE 'KALLIKREIN LOOP' OF THE GAMMA-NGF SUBUNITS WHICH RESULTS ...AN INTERNAL CLEAVAGE SITE EXISTS IN THE 'KALLIKREIN |
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Sequence details | THE RESIDUE NOMENCLATURE FOR THE ALPHA AND GAMMA SUBUNITS IS BASED ON THEIR ALIGNMENT WITH ...THE RESIDUE NOMENCLATU |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: DATA ARE VERY ANISOTROPIC | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.9 Details: PROTEIN WAS CRYSTALLIZED FROM 20MG/ML PROTEIN SOLUTION IN 50MM SODIUM PHOSPHATE (PH6.8) MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION (50MM SODIUM ACETATE PH4.5-5.1, 12-21% PEG 4000, 10 ...Details: PROTEIN WAS CRYSTALLIZED FROM 20MG/ML PROTEIN SOLUTION IN 50MM SODIUM PHOSPHATE (PH6.8) MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION (50MM SODIUM ACETATE PH4.5-5.1, 12-21% PEG 4000, 10 MICROMOLAR ZNSO4) (MCDONALD AND BLUNDELL, 1991, JMB, 219, 595-601)., pH 4.9 PH range: 5.0-5.1 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Type: EMBL/DESY, HAMBURG / Wavelength: 0.96 |
Detector | Detector: IMAGE PLATE / Date: May 1, 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 24209 / % possible obs: 96 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 3.1→3.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.427 / % possible all: 92.5 |
Reflection shell | *PLUS % possible obs: 92.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BETA-NGF AND PORCINE PANCREATIC KALLIKREIN (1BET AND 2PKA) Resolution: 3.15→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 Isotropic thermal model: ONE MAIN CHAIN AND ONE SI CHAIN TEMPERATURE FACTOR WERE REFINED PER RESIDUE Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 40.9 Å2
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Refine analyze | Luzzati d res low obs: 4.5 Å / Luzzati sigma a obs: 0.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.28 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.3623 |