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Yorodumi- PDB-2d4q: Crystal structure of the Sec-PH domain of the human neurofibromat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d4q | ||||||
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Title | Crystal structure of the Sec-PH domain of the human neurofibromatosis type 1 protein | ||||||
Components | Neurofibromin | ||||||
Keywords | SIGNALING PROTEIN / CRAL_TRIO / PH / TRITON x-100 / BETA HAIRPIN / Sec14 | ||||||
Function / homology | Function and homology information positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / gamma-aminobutyric acid secretion, neurotransmission / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / mast cell apoptotic process ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / gamma-aminobutyric acid secretion, neurotransmission / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / mast cell apoptotic process / negative regulation of mast cell proliferation / Schwann cell proliferation / vascular associated smooth muscle cell proliferation / mast cell proliferation / glutamate secretion, neurotransmission / negative regulation of Schwann cell proliferation / negative regulation of leukocyte migration / negative regulation of vascular associated smooth muscle cell migration / positive regulation of adenylate cyclase activity / regulation of cell-matrix adhesion / forebrain morphogenesis / negative regulation of neurotransmitter secretion / hair follicle maturation / cell communication / regulation of blood vessel endothelial cell migration / camera-type eye morphogenesis / smooth muscle tissue development / negative regulation of oligodendrocyte differentiation / sympathetic nervous system development / myelination in peripheral nervous system / myeloid leukocyte migration / phosphatidylcholine binding / peripheral nervous system development / phosphatidylethanolamine binding / metanephros development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of Ras protein signal transduction / collagen fibril organization / regulation of bone resorption / regulation of long-term synaptic potentiation / neural tube development / endothelial cell proliferation / forebrain astrocyte development / pigmentation / artery morphogenesis / regulation of postsynapse organization / regulation of synaptic transmission, GABAergic / negative regulation of neuroblast proliferation / negative regulation of MAPK cascade / adrenal gland development / negative regulation of protein import into nucleus / negative regulation of cell-matrix adhesion / spinal cord development / regulation of GTPase activity / Rac protein signal transduction / oligodendrocyte differentiation / negative regulation of osteoclast differentiation / negative regulation of endothelial cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of astrocyte differentiation / extrinsic apoptotic signaling pathway via death domain receptors / neuroblast proliferation / regulation of angiogenesis / Schwann cell development / negative regulation of stem cell proliferation / negative regulation of fibroblast proliferation / skeletal muscle tissue development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / extracellular matrix organization / negative regulation of angiogenesis / GTPase activator activity / negative regulation of cell migration / osteoclast differentiation / regulation of ERK1 and ERK2 cascade / phosphatidylinositol 3-kinase/protein kinase B signal transduction / liver development / negative regulation of MAP kinase activity / stem cell proliferation / long-term synaptic potentiation / regulation of long-term neuronal synaptic plasticity / negative regulation of protein kinase activity / wound healing / brain development / visual learning / cerebral cortex development / cognition / positive regulation of GTPase activity / osteoblast differentiation / Regulation of RAS by GAPs / protein import into nucleus / MAPK cascade / positive regulation of neuron apoptotic process / presynapse / heart development / cellular response to heat / fibroblast proliferation / actin cytoskeleton organization / regulation of gene expression Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.3 Å | ||||||
Authors | D'angelo, I. / Welti, S. / Bonneau, F. / Scheffzek, K. | ||||||
Citation | Journal: Embo Rep. / Year: 2006 Title: A novel bipartite phospholipid-binding module in the neurofibromatosis type 1 protein Authors: D'angelo, I. / Welti, S. / Bonneau, F. / Scheffzek, K. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Expression, purification and preliminary crystallographic characterization of a novel segment from the neurofibromatosis type 1 protein. Authors: Bonneau, F. / D'angelo, I. / Welti, S. / Ylanne, J. / Stier, G. / Scheffzek, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d4q.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d4q.ent.gz | 92.4 KB | Display | PDB format |
PDBx/mmJSON format | 2d4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/2d4q ftp://data.pdbj.org/pub/pdb/validation_reports/d4/2d4q | 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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Unit cell |
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-Components
#1: Protein | Mass: 29459.754 Da / Num. of mol.: 2 / Fragment: Sec14 homology domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: neurofibromin / Plasmid: PETM11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21359 #2: Chemical | #3: Chemical | #4: 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 |
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Crystal grow |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 5, 2002 / Details: Toroidal Zerodur mirror, radii of 4.9km and 79mm |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→15 Å / Num. obs: 37204 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rsym value: 0.07 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.3→2.48 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 17554 / Rsym value: 0.28 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 2.3→15 Å / Isotropic thermal model: overall / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Refmac, CNS
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.48 Å / Rfactor Rfree error: 0.01
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