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Yorodumi- PDB-7mj9: HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mj9 | |||||||||
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Title | HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / LYMPHOMA KINASE-DERIVED NEUROBLASTOMA TUMOR ANTIGEN / HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I / MHC-I / COMPLEX | |||||||||
Function / homology | Function and homology information cellular response to tumor cell / insulin-like growth factor binding / regulation of signal transduction / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding ...cellular response to tumor cell / insulin-like growth factor binding / regulation of signal transduction / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 / regulation of cell growth / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / collagen-containing extracellular matrix / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Toor, J.S. / Tripathi, S.M. / Truong, H.V. / Yarmarkovich, M. / Maris, J.M. / Sgourakis, N.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2021 Title: Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Authors: Yarmarkovich, M. / Marshall, Q.F. / Warrington, J.M. / Premaratne, R. / Farrel, A. / Groff, D. / Li, W. / di Marco, M. / Runbeck, E. / Truong, H. / Toor, J.S. / Tripathi, S. / Nguyen, S. / ...Authors: Yarmarkovich, M. / Marshall, Q.F. / Warrington, J.M. / Premaratne, R. / Farrel, A. / Groff, D. / Li, W. / di Marco, M. / Runbeck, E. / Truong, H. / Toor, J.S. / Tripathi, S. / Nguyen, S. / Shen, H. / Noel, T. / Church, N.L. / Weiner, A. / Kendsersky, N. / Martinez, D. / Weisberg, R. / Christie, M. / Eisenlohr, L. / Bosse, K.R. / Dimitrov, D.S. / Stevanovic, S. / Sgourakis, N.G. / Kiefel, B.R. / Maris, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mj9.cif.gz | 246.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mj9.ent.gz | 200.9 KB | Display | PDB format |
PDBx/mmJSON format | 7mj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mj9_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
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Full document | 7mj9_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 7mj9_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 7mj9_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/7mj9 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/7mj9 | HTTPS FTP |
-Related structure data
Related structure data | 7mj6C 7mj7C 7mj8C 7mjaC 5c07S 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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Unit cell |
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-Components
#1: Protein | Mass: 32082.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A*02:01 / Production host: Escherichia coli (E. coli) / References: UniProt: Q861F7 |
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#2: Protein | Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1032.342 Da / Num. of mol.: 1 / Fragment: Residues 14-22 / Mutation: Residue 18 mutated to arginine / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WX77 |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium Chloride, 0.1 M HEPES pH 7, 20 % PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03316 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→52.63 Å / Num. obs: 44403 / % possible obs: 98.4 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2298 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C07 Resolution: 1.75→52.63 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→52.63 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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