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Open data
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Basic information
Entry | Database: PDB / ID: 7mja | |||||||||
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Title | HLA-A*24:02 bound to Neuroblastoma derived PHOX2B peptide | |||||||||
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![]() | IMMUNE SYSTEM / NEUROBLASTOMA TUMOR ANTIGEN / PHOX2B / IGFBPL1 / HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I / MHC-I / COMPLEX | |||||||||
Function / homology | ![]() medullary reticular formation development / autonomic nervous system development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / hindbrain tangential cell migration ...medullary reticular formation development / autonomic nervous system development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / hindbrain tangential cell migration / noradrenergic neuron differentiation / cellular response to carbon dioxide / brainstem development / regulation of respiratory gaseous exchange by nervous system process / motor neuron migration / enteric nervous system development / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / glial cell differentiation / sympathetic nervous system development / type B pancreatic cell proliferation / cellular response to BMP stimulus / dopaminergic neuron differentiation / skeletal muscle cell differentiation / antigen processing and presentation / membrane depolarization / inner ear development / negative regulation of neuron differentiation / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of neuron differentiation / 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 / response to activity / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / 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 / sequence-specific double-stranded DNA binding / 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 / positive regulation of cold-induced thermogenesis / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Toor, J.S. / Tripathi, S.M. / Truong, H.V. / Yarmarkovich, M. / Maris, J.M. / Sgourakis, N.G. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 246.8 KB | Display | ![]() |
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PDB format | ![]() | 201.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 442 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mj6C ![]() 7mj7C ![]() 7mj8C ![]() 7mj9C ![]() 3vxnS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32466.869 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 / Fragment: UNP residues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein/peptide | Mass: 1140.268 Da / Num. of mol.: 1 / Fragment: Residues 43-51 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 10% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→87.43 Å / Num. obs: 60180 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.69→1.72 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3045 / CC1/2: 0.96 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VXN Resolution: 1.69→57.875 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.29 / 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: 1.69→57.875 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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