+Open data
-Basic information
Entry | Database: PDB / ID: 5vp7 | ||||||
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Title | Crystal structure of human KRAS G12A mutant in complex with GDP | ||||||
Components | GTPase KRas | ||||||
Keywords | HYDROLASE / Oncogenic mutant | ||||||
Function / homology | Function and homology information forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / positive regulation of glial cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / EGFR Transactivation by Gastrin / SHC1 events in EGFR signaling / Signalling to RAS / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC1 events in ERBB2 signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / 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 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by ERBB2 TMD/JMD mutants / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / FCERI mediated MAPK activation / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Ca2+ pathway / RAF/MAP kinase cascade / gene expression / actin cytoskeleton organization / Ras protein signal transduction / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Xu, S. / Long, B. / Boris, G. / Chen, A. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vp7.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vp7.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 5vp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vp7_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5vp7_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5vp7_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 5vp7_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/5vp7 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/5vp7 | HTTPS FTP |
-Related structure data
Related structure data | 5vpiC 5vpyC 5vpzC 5vq0C 5vq1C 5vq2C 5vq6C 5vq8C 5w22C 4i8gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 0 - 169 / Label seq-ID: 1 - 170
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AF
#1: Protein | Mass: 19407.867 Da / Num. of mol.: 2 / Fragment: residues 1-169 / Mutation: G12A, C118S 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 |
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-Non-polymers , 5 types, 208 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.95 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.2 mol L-1 sodium acetate, 0.1 mol L-1 Tris pH 8.5, 26% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | |||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 29, 2016 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.7→28.12 Å / Num. all: 43235 / Num. obs: 43235 / % possible obs: 99.9 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.038 / Rrim(I) all: 0.09 / Rsym value: 0.082 / Net I/σ(I): 10.8 / Num. measured all: 247335 | |||||||||||||||||||||||||||
Reflection shell | Rrim(I) all: 0.037 / Rsym value: 0.033 / Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I8G Resolution: 1.7→27.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.646 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.66 Å2 / Biso mean: 30.481 Å2 / Biso min: 13.43 Å2
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Refinement step | Cycle: final / Resolution: 1.7→27.07 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 1368 / Type: TIGHT THERMAL / Rms dev position: 0.92 Å / Weight position: 0.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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