[English] 日本語
![](img/lk-miru.gif)
- PDB-1nvx: Structural evidence for feedback activation by RasGTP of the Ras-... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1nvx | ||||||
---|---|---|---|---|---|---|---|
Title | Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS | ||||||
![]() |
| ||||||
![]() | SIGNALING PROTEIN / Proto-oncogene / GTP-binding / Guanine-nucleotide releasing factor | ||||||
Function / homology | ![]() 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 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of epidermal growth factor receptor signaling pathway / T-helper 1 type immune response / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of wound healing / leukocyte migration / regulation of T cell proliferation / positive regulation of miRNA metabolic process / 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 / neurotrophin TRK receptor signaling pathway / 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 / 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 / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Interleukin receptor SHC signaling / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / 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 / RAC1 GTPase cycle / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / 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 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / GTPase activator activity / guanyl-nucleotide exchange factor 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 GTPase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Margarit, S.M. / Sondermann, H. / Hall, B.E. / Nagar, B. / Hoelz, A. / Pirruccello, M. / Bar-Sagi, D. / Kuriyan, J. | ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 172.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 133.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 779.2 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 40.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nvuSC ![]() 1nvvC ![]() 1nvwC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
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
#1: Protein | Mass: 18861.166 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-166 / Mutation: A59G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 56532.730 Da / Num. of mol.: 1 Fragment: residues 566-10466, including the RAS GUANINE NUCLEOTIDE EXCHANGE FACTOR FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-GTP / | #5: Chemical | ChemComp-PO4 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75.2 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2-8% PEG 4000, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2001 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. all: 29067 / Num. obs: 29067 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 103.3 Å2 / Rsym value: 0.128 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 2966 / Rsym value: 0.542 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 255485 / Rmerge(I) obs: 0.128 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.542 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NVU Resolution: 3.2→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.1244 Å2 / ksol: 0.335659 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 89.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|