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Yorodumi- PDB-6jto: Crystal structure of HLA-C05 in complex with a tumor mut10m peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jto | ||||||
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Title | Crystal structure of HLA-C05 in complex with a tumor mut10m peptide | ||||||
Components |
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Keywords | IMMUNE SYSTEM / major histocompatibility complex / antigen / hla | ||||||
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 / TAP binding / 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 / secretory granule membrane / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / G protein activity / VEGFR2 mediated cell proliferation / positive regulation of receptor binding / early endosome lumen / Constitutive Signaling by EGFRvIII / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / RAF activation / regulation of long-term neuronal synaptic plasticity / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Signaling by high-kinase activity BRAF mutants / negative regulation of forebrain neuron differentiation / MAP2K and MAPK activation / visual learning / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / Signaling by SCF-KIT / HFE-transferrin receptor complex Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Bai, P. / Zhou, Q. / Wei, P. / Lei, Y. | ||||||
Citation | Journal: Sci China Life Sci / Year: 2021 Title: Rational discovery of a cancer neoepitope harboring the KRAS G12D driver mutation. Authors: Bai, P. / Zhou, Q. / Wei, P. / Bai, H. / Chan, S.K. / Kappler, J.W. / Marrack, P. / Yin, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jto.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jto.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 6jto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jto_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 6jto_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 6jto_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 6jto_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/6jto ftp://data.pdbj.org/pub/pdb/validation_reports/jt/6jto | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31776.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9TNN7, UniProt: P10321*PLUS |
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#2: Protein | Mass: 11616.964 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 874.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01116*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M ammonium acetate, 0.1M HEPES (pH 7.5), 25% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→56.678 Å / Num. obs: 49991 / % possible obs: 100 % / Redundancy: 2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.02672 / Net I/σ(I): 10.84 |
Reflection shell | Resolution: 1.7→1.761 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1885 / Num. unique obs: 4913 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→56.678 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→56.678 Å
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Refine LS restraints |
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LS refinement shell |
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