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Yorodumi- PDB-3d25: Crystal structure of HA-1 minor histocompatibility antigen bound ... -
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-Basic information
Entry | Database: PDB / ID: 3d25 | ||||||
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Title | Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC HLA-A2 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / MHC / HLA-A2 / SECONDARY ANCHOR RESIDUE / GLYCOPROTEIN / MINOR HISTOCOMPATIBILITY ANTIGEN / STEM CELL TRANSPLANTATION / Immune response | ||||||
Function / homology | Function and homology information : / neutrophil degranulation / activation of GTPase activity / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...: / neutrophil degranulation / activation of GTPase activity / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / RHOA GTPase cycle / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / RAC1 GTPase cycle / detection of bacterium / GTPase activator activity / T cell receptor binding / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / ruffle membrane / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / azurophil granule lumen / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / secretory granule lumen / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / intracellular signal transduction / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Nicholls, S. / Piper, K.P. / Mohammed, F. / Dafforn, T.R. / Tenzer, S. / Salim, M. / Mahendra, P. / Craddock, C. / van Endert, P. / Schild, H. ...Nicholls, S. / Piper, K.P. / Mohammed, F. / Dafforn, T.R. / Tenzer, S. / Salim, M. / Mahendra, P. / Craddock, C. / van Endert, P. / Schild, H. / Cobbold, M. / Engelhard, V.H. / Moss, P.A.H. / Willcox, B.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Secondary anchor polymorphism in the HA-1 minor histocompatibility antigen critically affects MHC stability and TCR recognition Authors: Nicholls, S. / Piper, K.P. / Mohammed, F. / Dafforn, T.R. / Tenzer, S. / Salim, M. / Mahendra, P. / Craddock, C. / van Endert, P. / Schild, H. / Cobbold, M. / Engelhard, V.H. / Moss, P.A. / Willcox, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d25.cif.gz | 185.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d25.ent.gz | 146.4 KB | Display | PDB format |
PDBx/mmJSON format | 3d25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d2/3d25 ftp://data.pdbj.org/pub/pdb/validation_reports/d2/3d25 | HTTPS FTP |
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-Related structure data
Related structure data | 1bd2S S: Starting model for refinement |
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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: 31725.088 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01892, UniProt: P04439*PLUS |
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#2: Protein | Mass: 11635.002 Da / Num. of mol.: 1 / Fragment: UNP residues 22-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769 |
#3: Protein/peptide | Mass: 1025.133 Da / Num. of mol.: 1 / Fragment: UNP residues 137-145 / Source method: obtained synthetically Details: The peptide is commercially synthesized. It is found naturally in humans. References: UniProt: Q6P189, UniProt: Q92619*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: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 20 % PEG 10K, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979355 |
Detector | Detector: ADSC / Date: Nov 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979355 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→42.033 Å / Num. obs: 108069 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.583 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BD2 Resolution: 1.3→20 Å / Num. parameters: 31647 / Num. restraintsaints: 39129 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.552 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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