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Yorodumi- PDB-2cik: Insights Into Crossreactivity in Human Allorecognition: The Struc... -
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-Basic information
Entry | Database: PDB / ID: 2cik | ||||||
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Title | Insights Into Crossreactivity in Human Allorecognition: The Structure of HLA-B35011 Presenting an Epitope derived from Cytochrome P450. | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PEPTIDE / ANTIGEN-PEPTIDE COMPLEX / MAJOR HISTOCOMPATIBILITY ANTIGEN / HUMAN / MHC / HLA / HLA-B3501 / EBV / ALLO-LIGAND / GLYCOPROTEIN / IMMUNE RESPONSE / MEMBRANE / MHC I / POLYMORPHISM / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / PYRROLIDONE CARBOXYLIC ACID / IMMUNE SYSTEM-PEPTIDE complex | ||||||
Function / homology | Function and homology information linoleic acid epoxygenase activity / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / Xenobiotics / regulation of interleukin-12 production / regulation of dendritic cell differentiation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / regulation of T cell anergy ...linoleic acid epoxygenase activity / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / Xenobiotics / regulation of interleukin-12 production / regulation of dendritic cell differentiation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / regulation of T cell anergy / regulation of interleukin-6 production / retinoic acid metabolic process / retinol metabolic process / unspecific monooxygenase / aromatase activity / 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 / detection of bacterium / xenobiotic metabolic process / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / monooxygenase activity / 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 / defense response / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / 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 / MHC class I protein complex / oxygen binding / 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 / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / iron ion binding / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Hourigan, C.S. / Harkiolaki, M. / Peterson, N.A. / Bell, J.I. / Jones, E.Y. / O'Callaghan, C.A. | ||||||
Citation | Journal: Eur.J.Immunol. / Year: 2006 Title: The Structure of the Human Allo-Ligand Hla-B3501 in Complex with a Cytochrome P450 Peptide: Steric Hindrance Influences Tcr Allo-Recognition. Authors: Hourigan, C.S. / Harkiolaki, M. / Peterson, N.A. / Bell, J.I. / Jones, E.Y. / O'Callaghan, C.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cik.cif.gz | 102.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cik.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/2cik ftp://data.pdbj.org/pub/pdb/validation_reports/ci/2cik | HTTPS FTP |
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-Related structure data
Related structure data | 1a1nS 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: 31940.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGM-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / Variant (production host): (DE3)PLYSS / References: UniProt: P30685, UniProt: O19626*PLUS | ||||
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#2: Protein | Mass: 11748.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGM-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / Variant (production host): (DE3)PLYSS / References: UniProt: P61769 | ||||
#3: Protein/peptide | Mass: 1027.259 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: PEPTIDE EPITOPE FROM HUMAN CYTOCHROME P450 ISOFORMS IIC8, IIC9, IIC10 AND IIC18 Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P33260*PLUS | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM BETA-2-MICROGLOBULIN IS THE ...INVOLVED IN THE PRESENTATI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % / Description: MODEL 1A1N WITH CHAIN C AND WATERS REMOVED. |
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Crystal grow | pH: 5.6 Details: 0.105M AMMONIUM ACETATE, 0.0525M TRI-SODIUM CITRATE DIHYDRATE PH 5.6 AND 15.75% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 30, 2001 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→20 Å / Num. obs: 47620 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 1.75→1.81 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A1N Resolution: 1.75→19.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.236 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→19.62 Å
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