+Open data
-Basic information
Entry | Database: PDB / ID: 1wq1 | ||||||
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Title | RAS-RASGAP COMPLEX | ||||||
Components |
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Keywords | COMPLEX (GTP-BINDING/GTPASE ACTIVATION) / RAS / GAP / SIGNAL TRANSDUCTION / GROWTH REGULATION / GTP HYDROLYSIS / TRANSITION STATE / COMPLEX (GTP-BINDING-GTPASE ACTIVATION) / COMPLEX (GTP-BINDING-GTPASE ACTIVATION) complex | ||||||
Function / homology | Function and homology information regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity ...regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / negative regulation of cell-matrix adhesion / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / mitotic cytokinesis / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / ephrin receptor signaling pathway / SHC-related events triggered by IGF1R / vasculogenesis / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / ruffle / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / phosphotyrosine residue binding / GTPase activator activity / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / animal organ morphogenesis / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Scheffzek, K. / Ahmadian, M.R. / Kabsch, W. / Wiesmueller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A. | ||||||
Citation | 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. / Wiesmuller, L. / Lautwein, A. / Schmitz, F. / Wittinghofer, A. #1: Journal: FEBS Lett. / Year: 1997 Title: The Interaction of Ras with Gtpase-Activating Proteins Authors: Wittinghofer, A. / Scheffzek, K. / Ahmadian, M.R. #2: 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. #3: Journal: Nature / Year: 1996 Title: Crystal 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. #4: 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. #5: Journal: Science / Year: 1987 Title: A Cytoplasmic Protein Stimulates Normal N-Ras P21 Gtpase, But Does not Affect Oncogenic Mutants Authors: Trahey, M. / Mccormick, F. #6: Journal: Cell(Cambridge,Mass.) / Year: 1986 Title: Biological and Biochemical Properties of Human Rash Genes Mutated at Codon 61 Authors: Der, C.J. / Finkel, T. / Cooper, G.M. #7: Journal: Nature / Year: 1984 Title: Biological Properties of Human C-Ha-Ras1 Genes Mutated at Codon 12 Authors: Seeburg, P.H. / Colby, W.W. / Capon, D.J. / Goeddel, D.V. / Levinson, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wq1.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wq1.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 1wq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wq/1wq1 ftp://data.pdbj.org/pub/pdb/validation_reports/wq/1wq1 | 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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-Components
-Protein , 2 types, 2 molecules RG
#1: Protein | Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 1 - 166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: H-RAS-1 / Organ: PLACENTA / Plasmid: PTRCGAP-334 / Gene (production host): GENE FRAGMENT OF P120GAP POSI / Production host: Escherichia coli (E. coli) / Strain (production host): CK 600 K / References: UniProt: P01112 |
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#2: Protein | Mass: 38223.277 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 714 - 1047 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOSOL / Gene: GENE FRAGMENT OF P120GAP POSI / Organ: PLACENTA / Plasmid: PTRCGAP-334 Gene (production host): GENE FRAGMENT OF P120GAP, POSITION 2258 - 3259 Production host: Escherichia coli (E. coli) / Strain (production host): DG103 / References: UniProt: P20936 |
-Non-polymers , 4 types, 38 molecules
#3: Chemical | ChemComp-MG / |
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#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-AF3 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: SEE REF. DESCRIBING THE STRUCTURE, pH 8. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Mar 14, 1997 / Details: FRANKS DOUBLE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 15811 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 41.9 Å2 / Rsym value: 0.06 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.35 / % possible all: 64 |
Reflection | *PLUS Num. measured all: 35339 / Rmerge(I) obs: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: RAS:GPPNP (PDB ENTRY 5P21), GAP-334 (PDB ENTRY 1WER) Resolution: 2.5→30 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 38.8 Å2
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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: 0.047 / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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