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Yorodumi- PDB-5vz5: Crystal structure of an anaplastic lymphoma kinase-derived neurob... -
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-Basic information
Entry | Database: PDB / ID: 5vz5 | ||||||
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Title | Crystal structure of an anaplastic lymphoma kinase-derived neuroblastoma tumor antigen bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501 | ||||||
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 : / ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity ...: / ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / response to environmental enrichment / ALK mutants bind TKIs / regulation of interleukin-12 production / swimming behavior / regulation of dendritic cell differentiation / regulation of T cell anergy / positive regulation of dendrite development / regulation of interleukin-6 production / regulation of neuron differentiation / Signaling by ALK / adult behavior / peptidyl-tyrosine autophosphorylation / TAP binding / protection from natural killer cell mediated cytotoxicity / neuron development / transmembrane receptor protein tyrosine kinase activity / negative regulation of lipid catabolic process / detection of bacterium / energy homeostasis / cell surface receptor protein tyrosine kinase signaling pathway / phosphorylation / secretory granule membrane / 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 / 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 / cellular response to iron ion / hippocampus development / receptor protein-tyrosine kinase / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / 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 / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / 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 / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / Signaling by ALK fusions and activated point mutants / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / early endosome membrane / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / heparin binding / regulation of cell population proliferation / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / protein tyrosine kinase activity / T cell differentiation in thymus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5901 Å | ||||||
Authors | Toor, J. / Rao, A.A. / Salama, S. / Tripathi, S. / Haussler, D. / Sgourakis, N.G. | ||||||
Citation | Journal: Front Immunol / Year: 2018 Title: A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Authors: Toor, J.S. / Rao, A.A. / McShan, A.C. / Yarmarkovich, M. / Nerli, S. / Yamaguchi, K. / Madejska, A.A. / Nguyen, S. / Tripathi, S. / Maris, J.M. / Salama, S.R. / Haussler, D. / Sgourakis, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vz5.cif.gz | 96.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vz5.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vz5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vz5_validation.pdf.gz | 470 KB | Display | wwPDB validaton report |
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Full document | 5vz5_full_validation.pdf.gz | 476.4 KB | Display | |
Data in XML | 5vz5_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 5vz5_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/5vz5 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/5vz5 | HTTPS FTP |
-Related structure data
Related structure data | 5txsC 6at9C 1xr8S 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32347.561 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P30464, UniProt: P01889*PLUS |
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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.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61769 |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1250.338 Da / Num. of mol.: 1 / Fragment: UNP Residues 1274-1283 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: B6D4Y8, UniProt: Q9UM73*PLUS, receptor protein-tyrosine kinase |
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-Non-polymers , 3 types, 36 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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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: 3.63 Å3/Da / Density % sol: 66 % / Description: Diamond shaped |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / Details: 0.1M Hepes (7.5) 2M Ammonium sulfate 2% PEG400 / PH range: 7.5-8.0 |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→97.77 Å / Num. obs: 21507 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.59→2.71 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2547 / CC1/2: 0.778 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XR8 Resolution: 2.5901→97.766 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5901→97.766 Å
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Refine LS restraints |
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LS refinement shell |
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