+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2cik | ||||||
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タイトル | Insights Into Crossreactivity in Human Allorecognition: The Structure of HLA-B35011 Presenting an Epitope derived from Cytochrome P450. | ||||||
要素 |
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キーワード | IMMUNE SYSTEM/PEPTIDE (免疫系) / ANTIGEN-PEPTIDE COMPLEX / MAJOR HISTOCOMPATIBILITY ANTIGEN / HUMAN (ヒト) / MHC / HLA / HLA-B3501 / EBV / ALLO-LIGAND / GLYCOPROTEIN (糖タンパク質) / IMMUNE RESPONSE (免疫応答) / MEMBRANE (生体膜) / MHC I / POLYMORPHISM / TRANSMEMBRANE (膜貫通型タンパク質) / IMMUNOGLOBULIN DOMAIN (免疫グロブリンフォールド) / PYRROLIDONE CARBOXYLIC ACID (ピログルタミン酸) / IMMUNE SYSTEM-PEPTIDE complex (免疫系) | ||||||
機能・相同性 | 機能・相同性情報 linoleic acid epoxygenase activity / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / 生体異物 / 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 / 生体異物 / 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 / retinoic acid metabolic process / regulation of interleukin-6 production / retinol metabolic process / 非特異的モノオキシゲナーゼ / 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 / negative regulation of forebrain neuron differentiation / defense response / 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 / 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 / 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 / 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 / 獲得免疫系 / learning or memory / 免疫応答 / iron ion binding / Amyloid fiber formation / lysosomal membrane / 小胞体 / external side of plasma membrane / ゴルジ体 / signaling receptor binding / focal adhesion / 自然免疫系 / intracellular membrane-bounded organelle / heme binding 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.75 Å | ||||||
データ登録者 | Hourigan, C.S. / Harkiolaki, M. / Peterson, N.A. / Bell, J.I. / Jones, E.Y. / O'Callaghan, C.A. | ||||||
引用 | ジャーナル: Eur.J.Immunol. / 年: 2006 タイトル: The Structure of the Human Allo-Ligand Hla-B3501 in Complex with a Cytochrome P450 Peptide: Steric Hindrance Influences Tcr Allo-Recognition. 著者: Hourigan, C.S. / Harkiolaki, M. / Peterson, N.A. / Bell, J.I. / Jones, E.Y. / O'Callaghan, C.A. | ||||||
履歴 |
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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. |
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 2cik.cif.gz | 102.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2cik.ent.gz | 78.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2cik.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | 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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-関連構造データ
関連構造データ | 1a1nS S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 31940.246 Da / 分子数: 1 / 断片: RESIDUES 25-300 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PGM-T7 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL-21 / Variant (発現宿主): (DE3)PLYSS / 参照: UniProt: P30685, UniProt: O19626*PLUS | ||||
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#2: タンパク質 | 分子量: 11748.160 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: PGM-T7 / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL-21 / Variant (発現宿主): (DE3)PLYSS / 参照: UniProt: P61769 | ||||
#3: タンパク質・ペプチド | 分子量: 1027.259 Da / 分子数: 1 / 由来タイプ: 合成 詳細: PEPTIDE EPITOPE FROM HUMAN CYTOCHROME P450 ISOFORMS IIC8, IIC9, IIC10 AND IIC18 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: P33260*PLUS | ||||
#4: 化合物 | #5: 水 | ChemComp-HOH / | 構成要素の詳細 | INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM BETA-2-MICROGLOBULIN IS THE ...INVOLVED IN THE PRESENTATI | |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.6 Å3/Da / 溶媒含有率: 53 % / 解説: MODEL 1A1N WITH CHAIN C AND WATERS REMOVED. |
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結晶化 | pH: 5.6 詳細: 0.105M AMMONIUM ACETATE, 0.0525M TRI-SODIUM CITRATE DIHYDRATE PH 5.6 AND 15.75% W/V PEG 4000 |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID14-3 / 波長: 0.93 |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2001年5月30日 / 詳細: MIRRORS |
放射 | モノクロメーター: DIAMOND / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.93 Å / 相対比: 1 |
反射 | 解像度: 1.75→20 Å / Num. obs: 47620 / % possible obs: 100 % / Observed criterion σ(I): 1 / 冗長度: 7.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.9 |
反射 シェル | 解像度: 1.75→1.81 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1A1N 解像度: 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 / 交差検証法: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.114 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 15.58 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.75→19.62 Å
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拘束条件 |
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