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- PDB-7l1c: Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7l1c | ||||||
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Title | Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide | ||||||
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![]() | IMMUNE SYSTEM / peptide major histocompatibility complex | ||||||
Function / homology | ![]() response to muscle inactivity / negative regulation of actin filament depolymerization / response to L-leucine / regulation of actin filament organization / response to butyrate / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / PI3K events in ERBB4 signaling / Activated NTRK2 signals through PI3K ...response to muscle inactivity / negative regulation of actin filament depolymerization / response to L-leucine / regulation of actin filament organization / response to butyrate / autosome genomic imprinting / IRS-mediated signalling / cellular response to hydrostatic pressure / PI3K events in ERBB4 signaling / Activated NTRK2 signals through PI3K / positive regulation of protein localization to membrane / Activated NTRK3 signals through PI3K / negative regulation of fibroblast apoptotic process / cardiac muscle cell contraction / phosphatidylinositol 3-kinase complex, class IB / vasculature development / Signaling by cytosolic FGFR1 fusion mutants / regulation of cellular respiration / phosphatidylinositol 3-kinase complex, class IA / anoikis / phosphatidylinositol 3-kinase complex / Nephrin family interactions / Costimulation by the CD28 family / relaxation of cardiac muscle / 1-phosphatidylinositol-4-phosphate 3-kinase activity / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / MET activates PI3K/AKT signaling / PI3K/AKT activation / phosphatidylinositol-4,5-bisphosphate 3-kinase / vascular endothelial growth factor signaling pathway / phosphatidylinositol 3-kinase / T cell mediated cytotoxicity directed against tumor cell target / phosphatidylinositol-3-phosphate biosynthetic process / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 1-phosphatidylinositol-3-kinase activity / Signaling by ALK / Golgi medial cisterna / negative regulation of macroautophagy / positive regulation of CD8-positive, alpha-beta T cell proliferation / PI-3K cascade:FGFR3 / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / CD8 receptor binding / PI-3K cascade:FGFR2 / response to dexamethasone / PI-3K cascade:FGFR4 / protein kinase activator activity / PI-3K cascade:FGFR1 / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / CD28 dependent PI3K/Akt signaling / Synthesis of PIPs at the plasma membrane / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / PI3K events in ERBB2 signaling / TAP binding / negative regulation of anoikis / RET signaling / intercalated disc / regulation of multicellular organism growth / insulin receptor substrate binding / protection from natural killer cell mediated cytotoxicity / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K Cascade / positive regulation of TOR signaling / endothelial cell migration / RAC2 GTPase cycle / Role of phospholipids in phagocytosis / GAB1 signalosome / Role of LAT2/NTAL/LAB on calcium mobilization / beta-2-microglobulin binding / Interleukin receptor SHC signaling / adipose tissue development / phagocytosis / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / T cell receptor binding / energy homeostasis / positive regulation of lamellipodium assembly / Signaling by FGFR4 in disease / cardiac muscle contraction / detection of bacterium / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR3 in disease / Tie2 Signaling / GPVI-mediated activation cascade / Signaling by FGFR2 in disease / T cell costimulation / RAC1 GTPase cycle / response to muscle stretch / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / Downstream signal transduction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, J. / Baker, B.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA. Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / ...Authors: Chandran, S.S. / Ma, J. / Klatt, M.G. / Dundar, F. / Bandlamudi, C. / Razavi, P. / Wen, H.Y. / Weigelt, B. / Zumbo, P. / Fu, S.N. / Banks, L.B. / Yi, F. / Vercher, E. / Etxeberria, I. / Bestman, W.D. / Da Cruz Paula, A. / Aricescu, I.S. / Drilon, A. / Betel, D. / Scheinberg, D.A. / Baker, B.M. / Klebanoff, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.4 KB | Display | ![]() |
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PDB format | ![]() | 141.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l1bC ![]() 7l1dC ![]() 7rrgC ![]() 2xpgS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31628.838 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 972.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 323 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
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![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.57 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: 20% w/v Polyethylene glycol 3,350, 200 mM Ammonium formate, pH 6.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 44346 / % possible obs: 99.86 % / Redundancy: 17.6 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.029 / Rrim(I) all: 0.127 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 1.96→1.99 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.918 / Num. unique obs: 2187 / CC1/2: 0.8 / Rpim(I) all: 0.267 / Rrim(I) all: 0.96 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2XPG Resolution: 1.96→44.95 Å / SU ML: 0.2236 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.7119 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→44.95 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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