+Open data
-Basic information
Entry | Database: PDB / ID: 8oso | ||||||
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Title | GTPase HRAS in complex with Zn-cyclen under 500 MPa pressure | ||||||
Components | GTPase HRasHRAS | ||||||
Keywords | ONCOPROTEIN / G PROTEIN / SIGNALING PROTEIN / HPMX | ||||||
Function / homology | Function and homology information GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / positive regulation of protein targeting to membrane / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / 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 / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / Signaling by RAF1 mutants / GDP binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / positive regulation of type II interferon production / cellular senescence / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Colloc'h, N. / Prange, T. / Girard, E. / Kalbitzer, H.R. | ||||||
Funding support | 1items
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Citation | Journal: Chemistry / Year: 2024 Title: High pressure promotes binding of the allosteric inhibitor Zn2+-cyclen in crystals of activated H-Ras. Authors: Girard, E. / Lopes, P. / Spoerner, M. / Dhaussy, A.C. / Prange, T. / Kalbitzer, H.R. / Colloc'h, N. #1: Journal: Chem Sci / Year: 2022 Title: Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography. Authors: Girard, E. / Lopes, P. / Spoerner, M. / Dhaussy, A.C. / Prange, T. / Kalbitzer, H.R. / Colloc'h, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8oso.cif.gz | 56.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oso.ent.gz | 33.6 KB | Display | PDB format |
PDBx/mmJSON format | 8oso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/8oso ftp://data.pdbj.org/pub/pdb/validation_reports/os/8oso | HTTPS FTP |
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-Related structure data
Related structure data | 8osmC 8osnC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: GTPase HRAS N-terminally processed Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pTac / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P01112, small monomeric GTPase |
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-Non-polymers , 6 types, 45 molecules
#2: Chemical | ChemComp-GNP / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-PGE / |
#5: Chemical | ChemComp-YCN / |
#6: Chemical | ChemComp-ZN / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.5 Details: 40 MM TRIS HCL, 10 MM MGCL2, 2 MM DTE, 26-30 % PEG-400 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: CRISTAL / Wavelength: 0.51035 Å |
Detector | Type: RAYONIX SX-165mm / Detector: CCD / Date: Jul 22, 2015 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.51035 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→33.46 Å / Num. obs: 4948 / % possible obs: 95.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 25.89 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.117 / Rrim(I) all: 0.23 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.5→2.64 Å / % possible obs: 93.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.918 / Num. measured all: 2360 / Num. unique obs: 678 / CC1/2: 0.429 / Rpim(I) all: 0.56 / Rrim(I) all: 1.082 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→32.73 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1779 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.21 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→32.73 Å
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Refine LS restraints |
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LS refinement shell |
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