+Open data
-Basic information
Entry | Database: PDB / ID: 1nf1 | ||||||
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Title | THE GAP RELATED DOMAIN OF NEUROFIBROMIN | ||||||
Components | PROTEIN (NEUROFIBROMIN) | ||||||
Keywords | SIGNALING PROTEIN / NEUROFIBROMIN / TYPE I NEUROFIBROMATOSIS / NF1 / RAS / GAP / SIGNAL TRANSDUCTION / CANCER / GROWTH REGULATION / GTP HYDROLYSIS / PATIENT MUTATION / ARGININE FINGER | ||||||
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 / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / gamma-aminobutyric acid secretion, neurotransmission / negative regulation of mast cell proliferation ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / gamma-aminobutyric acid secretion, neurotransmission / negative regulation of mast cell proliferation / mast cell apoptotic process / 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 / smooth muscle tissue development / camera-type eye morphogenesis / negative regulation of oligodendrocyte differentiation / sympathetic nervous system development / peripheral nervous system development / myelination in peripheral nervous system / myeloid leukocyte migration / phosphatidylcholine binding / 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 / artery morphogenesis / regulation of postsynapse organization / regulation of synaptic transmission, GABAergic / negative regulation of neuroblast proliferation / adrenal gland development / negative regulation of protein import into nucleus / negative regulation of MAPK cascade / negative regulation of cell-matrix adhesion / pigmentation / regulation of GTPase activity / spinal cord development / 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 / regulation of ERK1 and ERK2 cascade / Schwann cell development / negative regulation of angiogenesis / negative regulation of stem cell proliferation / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / skeletal muscle tissue development / negative regulation of MAP kinase activity / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / extracellular matrix organization / osteoclast differentiation / positive regulation of GTPase activity / liver development / negative regulation of cell migration / stem cell proliferation / long-term synaptic potentiation / negative regulation of protein kinase activity / regulation of long-term neuronal synaptic plasticity / wound healing / visual learning / brain development / cognition / cerebral cortex development / Regulation of RAS by GAPs / osteoblast differentiation / protein import into nucleus / positive regulation of neuron apoptotic process / MAPK cascade / presynapse / regulation of gene expression / heart development / cellular response to heat / fibroblast proliferation / actin cytoskeleton organization Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å | ||||||
Authors | Scheffzek, K. / Ahmadian, M.R. / Wiesmueller, L. / Kabsch, W. / Stege, P. / Schmitz, F. / Wittinghofer, A. | ||||||
Citation | Journal: EMBO J. / Year: 1998 Title: Structural analysis of the GAP-related domain from neurofibromin and its implications. Authors: Scheffzek, K. / Ahmadian, M.R. / Wiesmuller, L. / Kabsch, W. / Stege, P. / Schmitz, F. / Wittinghofer, A. #1: Journal: Science / Year: 1997 Title: The Ras-Rasgap Complex: Structural Basis for Gtpase Activation and its Loss in Oncogenic Ras Mutants Authors: Scheffzek, K. / Ahmadian, M.R. / Kabsch, W. / Wiesmueller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A. #2: Journal: Nat.Struct.Biol. / Year: 1997 Title: Confirmation of the Arginine-Finger Hypothesis for the Gap-Stimulated GTP- Hydrolysis Reaction of Ras Authors: Ahmadian, M.R. / Stege, P. / Scheffzek, K. / Wittinghofer, A. #3: Journal: J.Biol.Chem. / Year: 1996 Title: Structural Differences in the Minimal Catalytic Domains of the Gtpasse- Activating Proteins P120Gap and Neurofibromin Authors: Ahmadian, M.R. / Wiesmueller, L. / Lautwein, A. / Bischoff, F.R. / Wittinghofer, A. #4: Journal: Nature / Year: 1996 Title: 3-Dimensional Structure of the Gtpase Activating Domain of Human P120Gap and Implications for the Interaction with Ras Authors: Scheffzek, K. / Lautwein, A. / Kabsch, W. / Ahmadian, M.R. / Wittinghofer, A. #5: Journal: Science / Year: 1996 Title: Formation of a Transition-State Analog of the Ras Gtpase Reaction by Ras:Gdp, Tetrafluoroaluminate and Gtpase-Activating Proteins Authors: Mittal, R. / Ahmadian, M.R. / Goody, R.S. / Wittinghofer, A. #6: Journal: Neuron / Year: 1993 Title: The Neurofibromatosis Type I Gene and its Protein Product Authors: Gutmann, D.H. / Collins, F.S. #7: Journal: Cell(Cambridge,Mass.) / Year: 1990 Title: The NF1 Locus Encodes a Protein Functionally Related to Mammalian Gap and Yeast Ira Proteins Authors: Ballester, R. / Marchuk, D. / Boguski, M. / Saulino, A. / Letcher, R. / Wigler, M. / Collins, F. #8: Journal: Cell(Cambridge,Mass.) / Year: 1990 Title: The Gap-Related Domain of the Neurofibromatosis Type I Gene Product Interacts with Ras P21 Authors: Martin, G.A. / Viskochil, D. / Bollag, G. / Mccabe, P.C. / Crosier, W.J. / Hausbruck, H. / Conroy, L. / Clark, R. / O'Connell, P. / Cawthon, R.M. / Innis, M.A. / Mccormick, F. #9: Journal: Cell(Cambridge,Mass.) / Year: 1990 Title: The Catalytic Domain of the Neurofibromatosis Type I Gene Product Stimulates Ras Gtpase and Complements Ira Mutants of S. Cerevisiae Authors: Xu, G. / Lin, B. / Tanaka, K. / Dunn, D. / Wod, D. / Gesteland, R. / White, R. / Weiss, R. / Tamanoi, F. #10: Journal: Embo J. / Year: 1990 Title: Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 A Resolution: Implications for the Mechanism of GTP Hydrolysis Authors: Pai, E.F. / Krengel, U. / Petsko, G.A. / Goody, R.S. / Kabsch, W. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nf1.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nf1.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nf1_validation.pdf.gz | 367.9 KB | Display | wwPDB validaton report |
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Full document | 1nf1_full_validation.pdf.gz | 374.2 KB | Display | |
Data in XML | 1nf1_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1nf1_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nf1 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nf1 | HTTPS FTP |
-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: 37982.672 Da / Num. of mol.: 1 / Fragment: GAP RELATED DOMAIN Source method: isolated from a genetically manipulated source Details: SEE REF.5 FOR DETAILS / Source: (gene. exp.) Homo sapiens (human) / Description: S. REF. 4 / Cellular location: CYTOSOL / Plasmid: PETNF1-333 / Production host: Escherichia coli (E. coli) / Strain (production host): DG103 / References: UniProt: P21359 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 6 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.98 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: S. REF. DESCRIBING THE STRUCTURE, pH 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
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 / Beamline: X11 / Wavelength: 0.91 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→100 Å / Num. obs: 50172 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.6 / % possible all: 99.8 |
Reflection | *PLUS Num. obs: 11665 / % possible obs: 99.8 % / Num. measured all: 50172 / Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.5→30 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED IN FINAL STAGES
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Displacement parameters | Biso mean: 47.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.5 Å / Rfactor Rfree: 0.436 / % reflection Rfree: 11.9 % / Rfactor Rwork: 0.4 |