+Open data
-Basic information
Entry | Database: PDB / ID: 4uru | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of H-Ras and SOS in complex with ligands | ||||||
Components |
| ||||||
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 / oncogene-induced cell senescence / Activation of RAC1 / positive regulation of ruffle assembly / blood vessel morphogenesis / Signaling by LTK / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / epidermal growth factor receptor binding / T-helper 1 type immune response / positive regulation of wound healing / leukocyte migration / regulation of T cell proliferation / NRAGE signals death through JNK / roof of mouth development / eyelid development in camera-type eye / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / Fc-epsilon receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / RAS signaling downstream of NF1 loss-of-function variants / neurotrophin TRK receptor signaling pathway / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / positive regulation of protein targeting to membrane / Signalling to RAS / 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 / Interleukin receptor SHC signaling / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / RAC1 GTPase cycle / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / myelination / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / GTPase activator activity / insulin-like growth factor receptor signaling pathway / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of epithelial cell proliferation Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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.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. / ...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. / Kettle, J.G. / Nowak, T. / Overman, R. / Patel, S.J. / Perkins, P. / Spadola, L. / Tart, J. / Tucker, J.A. / Wrigley, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4uru.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4uru.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 4uru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/4uru ftp://data.pdbj.org/pub/pdb/validation_reports/ur/4uru | HTTPS FTP |
---|
-Related structure data
Related structure data | 4urvC 4urwC 4urxC 4uryC 4urzC 4us0C 4us1C 4us2C C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#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 | ChemComp-6W2 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.53 % / Description: NONE |
---|---|
Crystal grow | Details: 3.2M SODIUM FORMATE, 2% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→119.74 Å / Num. obs: 27510 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 74.95 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.7 |
Reflection shell | Resolution: 2.83→2.98 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.6 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 2.83→105.56 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.8981 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.456 / SU Rfree Blow DPI: 0.285
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.89 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→105.56 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.83→2.94 Å / Total num. of bins used: 14
|