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- 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. | ||||||
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![]() | 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 | ![]() linoleic acid epoxygenase activity / arachidonate 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 / arachidonate 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 / retinol metabolic process / retinoic acid metabolic process / unspecific monooxygenase / aromatase activity / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / monooxygenase activity / xenobiotic metabolic process / 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 / 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 / oxygen binding / 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 / 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 / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / iron ion binding / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / focal adhesion / heme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hourigan, C.S. / Harkiolaki, M. / Peterson, N.A. / Bell, J.I. / Jones, E.Y. / O'Callaghan, C.A. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 102.8 KB | Display | ![]() |
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PDB format | ![]() | 78.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | 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 |
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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: 31940.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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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.) ![]() ![]() ![]() | ||||
#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.) ![]() | ||||
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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