+Open data
-Basic information
Entry | Database: PDB / ID: 7c41 | ||||||
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Title | KRAS G12V and H-REV107 peptide complex | ||||||
Components |
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Keywords | ONCOPROTEIN/HYDROLASE / KRAS G12V / H-REV107 / inhibitor / STRUCTURAL PROTEIN / ONCOPROTEIN-HYDROLASE complex | ||||||
Function / homology | Function and homology information membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity ...membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / peroxisome organization / N-acyltransferase activity / phospholipid biosynthetic process / phospholipase A2 activity / lens fiber cell differentiation / phospholipase A2 / peroxisomal membrane / forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / triglyceride metabolic process / acyltransferase activity / 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 / 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 / localization / Signalling to RAS / SHC-related events triggered by IGF1R / glial cell proliferation / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / phospholipid metabolic process / 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 / lipid catabolic process / 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 CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / 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 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / mitochondrial membrane / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / response to bacterium / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.276 Å | ||||||
Authors | Han, C.W. / Jeong, M.S. / Jang, S.B. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Cancers (Basel) / Year: 2020 Title: A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants. Authors: Han, C.W. / Jeong, M.S. / Ha, S.C. / Jang, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c41.cif.gz | 151.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c41.ent.gz | 118.1 KB | Display | PDB format |
PDBx/mmJSON format | 7c41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7c41_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 7c41_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 7c41_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 7c41_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/7c41 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/7c41 | HTTPS FTP |
-Related structure data
Related structure data | 7c3zC 7c40C 5uqwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 20013.539 Da / Num. of mol.: 4 / Mutation: G12V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01116 #2: Protein/peptide | | Mass: 1131.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: P53816, phospholipase A1, phospholipase A2 #3: Chemical | ChemComp-GDP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.18 Å3/Da / Density % sol: 61.31 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: polyethylene glycol 3350, 0.2 M potassium nitrate at pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. obs: 45859 / % possible obs: 97.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.27→2.3284 Å / Rmerge(I) obs: 0.2 / Num. unique obs: 2465 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UQW Resolution: 2.276→36.522 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 29.35
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.276→36.522 Å
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Refine LS restraints |
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LS refinement shell |
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