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Yorodumi- PDB-6hby: HLA class II peptide flanking residues tune the immunogenicity of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hby | ||||||
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Title | HLA class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HLA Class II / MHC II / Human / 5T4 tumor epitope | ||||||
Function / homology | Function and homology information mesenchymal cell migration / dendrite arborization / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ...mesenchymal cell migration / dendrite arborization / regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of chemotaxis / olfactory learning / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / synaptic transmission, GABAergic / positive regulation of synapse assembly / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / axon terminus / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / cell chemotaxis / trans-Golgi network membrane / protein localization to plasma membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / negative regulation of canonical Wnt signaling pathway / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / immune response / positive regulation of protein phosphorylation / lysosomal membrane / negative regulation of cell population proliferation / external side of plasma membrane / Golgi membrane / dendrite / positive regulation of DNA-templated transcription / cell surface / endoplasmic reticulum / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | MacLachlan, B. / Rizkallah, P.J. / Sewell, A.K. / Cole, D.K. / Godkin, A.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Human leukocyte antigen (HLA) class II peptide flanking residues tune the immunogenicity of a human tumor-derived epitope. Authors: MacLachlan, B.J. / Dolton, G. / Papakyriakou, A. / Greenshields-Watson, A. / Mason, G.H. / Schauenburg, A. / Besneux, M. / Szomolay, B. / Elliott, T. / Sewell, A.K. / Gallimore, A. / ...Authors: MacLachlan, B.J. / Dolton, G. / Papakyriakou, A. / Greenshields-Watson, A. / Mason, G.H. / Schauenburg, A. / Besneux, M. / Szomolay, B. / Elliott, T. / Sewell, A.K. / Gallimore, A. / Rizkallah, P. / Cole, D.K. / Godkin, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hby.cif.gz | 256.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hby.ent.gz | 213.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hby.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/6hby ftp://data.pdbj.org/pub/pdb/validation_reports/hb/6hby | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
-HLA class II histocompatibility antigen, DR alpha ... , 2 types, 2 molecules AD
#1: Protein | Mass: 20727.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Variant: *01:01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903 |
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#4: Protein | Mass: 20971.670 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Variant: *01:01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903 |
-Protein / Protein/peptide , 2 types, 4 molecules BECF
#2: Protein | Mass: 22211.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Variant: *01:01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS #3: Protein/peptide | Mass: 2008.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13641*PLUS |
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-Non-polymers , 3 types, 316 molecules
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PO4 / #7: 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: 2.52 Å3/Da / Density % sol: 51.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane pH 7.5, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→60.64 Å / Num. obs: 64792 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 31.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.144 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.913 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4807 / CC1/2: 0.589 / Rrim(I) all: 1.295 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→60.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.678 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.159 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.763 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→60.64 Å
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Refine LS restraints |
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