|Entry||Database: PDB / ID: 5vq2|
|Title||Crystal structure of human WT-KRAS in complex with GTP|
|Function / homology|
Function and homology information
endocrine signaling / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / positive regulation of Rac protein signal transduction / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of glial cell proliferation ...endocrine signaling / forebrain astrocyte development / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / positive regulation of Rac protein signal transduction / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of glial cell proliferation / Signaling by RAS GTPase mutants / Signaling by RAS GAP mutants / Activation of RAS in B cells / RUNX3 regulates p14-ARF / 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 / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Estrogen-stimulated signaling through PRKCZ / homeostasis of number of cells within a tissue / Signaling by PDGFRA extracellular domain mutants / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / SHC-mediated cascade:FGFR3 / Signaling by FGFR4 in disease / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR4 / Signaling by FLT3 ITD and TKD mutants / SHC-mediated cascade:FGFR1 / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Tie2 Signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / G protein activity / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in EGFR signaling / p38MAPK events / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / small monomeric GTPase / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / NCAM signaling for neurite out-growth / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / visual learning / regulation of long-term neuronal synaptic plasticity / RAF activation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Ca2+ pathway / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / extrinsic component of cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / GDP binding / Negative regulation of MAPK pathway / regulation of protein stability / RAS processing / Signaling by RAF1 mutants / actin cytoskeleton organization / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by moderate kinase activity BRAF mutants / Signaling by BRAF and RAF1 fusions / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ras protein signal transduction / neuron apoptotic process / RAF/MAP kinase cascade / mitochondrial outer membrane / negative regulation of neuron apoptotic process / GTPase activity / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTPase KRas
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å|
|Authors||Xu, S. / Long, B. / Boris, G. / Ni, S. / Kennedy, M.A.|
|Citation||Journal: Acta Crystallogr D Struct Biol / Year: 2017|
Title: Structural insight into the rearrangement of the switch I region in GTP-bound G12A K-Ras.
Authors: Xu, S. / Long, B.N. / Boris, G.H. / Chen, A. / Ni, S. / Kennedy, M.A.
|Structure viewer||Molecule: |
Downloads & links
A: GTPase KRas
B: GTPase KRas
A: GTPase KRas
B: GTPase KRas
|Noncrystallographic symmetry (NCS)||NCS domain: |
NCS domain segments:
Mass: 19393.842 Da / Num. of mol.: 2 / Fragment: residues 1-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116
Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
|#3: Chemical||#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.71 Å3/Da / Density % sol: 54.64 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, hanging drop|
Details: 0.2 mol/L sodium acetate, 0.1 mol/L Tris pH 8.5, 28% PEG 3,350
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å|
|Detector||Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 5, 2017|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.97931 Å / Relative weight: 1|
|Reflection||Resolution: 1.96→67.91 Å / Num. obs: 29024 / % possible obs: 99.8 % / Redundancy: 5.3 % / Rpim(I) all: 0.073 / Rrim(I) all: 0.169 / Rsym value: 0.14 / Net I/av σ(I): 3.9 / Net I/σ(I): 6.6|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→67.91 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.549 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.145 |
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å|
|Displacement parameters||Biso max: 115.29 Å2 / Biso mean: 32.908 Å2 / Biso min: 12.76 Å2|
|Refinement step||Cycle: final / Resolution: 1.96→67.91 Å|
|Refine LS restraints|
|Refine LS restraints NCS||Number: 1282 / Type: TIGHT THERMAL / Rms dev position: 1.45 Å / Weight position: 0.5|
|LS refinement shell||Resolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20 |
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