[English] 日本語
Yorodumi- PDB-1nvv: Structural evidence for feedback activation by RasGTP of the Ras-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nvv | ||||||
---|---|---|---|---|---|---|---|
Title | Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / Proto-oncogene / GTP-binding / Guanine-nucleotide releasing factor | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.18 Å | ||||||
Authors | Margarit, S.M. / Sondermann, H. / Hall, B.E. / Nagar, B. / Hoelz, A. / Pirruccello, M. / Bar-Sagi, D. / Kuriyan, J. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2003 Title: Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS Authors: Margarit, S.M. / Sondermann, H. / Hall, B.E. / Nagar, B. / Hoelz, A. / Pirruccello, M. / Bar-Sagi, D. / Kuriyan, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nvv.cif.gz | 186 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nvv.ent.gz | 143.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nv/1nvv ftp://data.pdbj.org/pub/pdb/validation_reports/nv/1nvv | HTTPS FTP |
---|
-Related structure data
Related structure data | 1nvuSC 1nvwC 1nvxC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| x 8||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Details | Two molecules of Ras bound to one molecule of Sos, one at the active site (chainID, R) and the other at a distal site (chainID, Q). The distal Ras has GTP bound to it, while the active site Ras is nucleotide-free. |
-Components
-Transforming protein p21/H-RAS- ... , 2 types, 2 molecules QR
#1: Protein | Mass: 18783.096 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 / Mutation: Y64A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS OR HRAS1 / Plasmid: p-ProEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01112 |
---|---|
#2: Protein | Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS OR HRAS1 / Plasmid: p-ProEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01112 |
-Protein , 1 types, 1 molecules S
#3: Protein | Mass: 56532.730 Da / Num. of mol.: 1 Fragment: residues 566-1046, including RAS GUANINE NUCLEOTIDE EXCHANGE FACTOR FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Plasmid: p-ProEXHT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07889 |
---|
-Non-polymers , 4 types, 322 molecules
#4: Chemical | ChemComp-MG / | ||||
---|---|---|---|---|---|
#5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-GNP / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.93 Å3/Da / Density % sol: 68.42 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.2-1.5 M phosphate, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2002 / Details: mirrors |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.18→64.19 Å / Num. all: 74722 / Num. obs: 74722 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 19.7 Å2 / Rsym value: 0.103 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.18→2.26 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 6315 / Rsym value: 0.352 / % possible all: 81.9 |
Reflection | *PLUS Lowest resolution: 64 Å / Num. measured all: 329000 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 81.9 % / Rmerge(I) obs: 0.352 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NVU Resolution: 2.18→64.19 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.8609 Å2 / ksol: 0.374455 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→64.19 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.18→2.32 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 64 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|