+Open data
-Basic information
Entry | Database: PDB / ID: 4urv | ||||||
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Title | The crystal structure of H-Ras and SOS in complex with ligands | ||||||
Components |
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Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of epidermal growth factor receptor signaling pathway / T-helper 1 type immune response / epidermal growth factor receptor binding / Regulation of KIT signaling / positive regulation of wound healing / positive regulation of miRNA metabolic process / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / eyelid development in camera-type eye / defense response to protozoan / Fc-epsilon receptor signaling pathway / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / positive regulation of protein targeting to membrane / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / Interleukin receptor SHC signaling / 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 / RAC1 GTPase cycle / 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 / FCERI mediated Ca+2 mobilization / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / GTPase activator activity / guanyl-nucleotide exchange factor activity / small monomeric GTPase / insulin-like growth factor receptor signaling pathway / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Winter, J.J.G. / Anderson, M. / Blades, K. / Brassington, C. / Breeze, A.L. / Chresta, C. / Embrey, K. / Fairley, G. / Faulder, P. / Finlay, M.R.V. ...Winter, J.J.G. / Anderson, M. / Blades, K. / Brassington, C. / Breeze, A.L. / Chresta, C. / Embrey, K. / Fairley, G. / Faulder, P. / Finlay, M.R.V. / Kettle, J.G. / Nowak, T. / Overman, R. / Patel, S.J. / Perkins, P. / Spadola, L. / Tart, J. / Tucker, J. / Wrigley, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Small Molecule Binding Sites on the Ras:SOS Complex Can be Exploited for Inhibition of Ras Activation. Authors: Winter, J. / Anderson, M. / Blades, K. / Chresta, C. / Embrey, K.J. / Fairley, G. / Faulder, P. / Finlay, M.R.V. / Kettle, J.G. / Nowak, T. / Overman, R. / Patel, S.J. / Perkins, P. / ...Authors: Winter, J. / Anderson, M. / Blades, K. / Chresta, C. / Embrey, K.J. / Fairley, G. / Faulder, P. / Finlay, M.R.V. / Kettle, J.G. / Nowak, T. / Overman, R. / Patel, S.J. / Perkins, P. / Spadola, L. / Tart, J. / Tucker, J.A. / Wrigley, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4urv.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4urv.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 4urv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/4urv ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4urv | HTTPS FTP |
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-Related structure data
Related structure data | 4uruC 4urwC 4urxC 4uryC 4urzC 4us0C 4us1C 4us2C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21083.557 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01112 | ||||
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#2: Protein | Mass: 57177.426 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 564-1049 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q07889 | ||||
#3: Chemical | #4: Chemical | ChemComp-UMK / | #5: 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: 3.59 Å3/Da / Density % sol: 65.76 % / Description: NONE |
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Crystal grow | Details: 3.2M SODIUM FORMATE, 2% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→50.05 Å / Num. obs: 35041 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 66.18 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.58→2.67 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.5 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→48.48 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.305 / SU Rfree Blow DPI: 0.23
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Displacement parameters | Biso mean: 53.99 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→48.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.58→2.65 Å / Total num. of bins used: 18
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