+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3mrl | ||||||
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タイトル | Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide C6V variant | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / MHC class I (MHCクラスI分子) / HLA / IMMUNE RESPONSE (免疫応答) / NONAPEPTIDE (ペプチド) / VIRAL PEPTIDE / HEPATITIS C VIRUS (C型肝炎ウイルス) / NS3 PROTEIN | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of triglyceride biosynthetic process / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 ...positive regulation of triglyceride biosynthetic process / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / detection of bacterium / 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 / MHC class I protein complex / SH3 domain 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 / 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 / nucleoside-triphosphate phosphatase / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / protein complex oligomerization / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / monoatomic ion channel activity / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / viral nucleocapsid / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / RNA helicase activity 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Hepatitis C virus genotype 1b | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.41 Å | ||||||
データ登録者 | Gras, S. / Reiser, J.-B. / Chouquet, A. / Le Gorrec, M. / Debeaupuis, E. / Echasserieau, K. / Saulquin, X. / Bonneville, M. / Housset, D. | ||||||
引用 | ジャーナル: J.Immunol. / 年: 2014 タイトル: Analysis of Relationships between Peptide/MHC Structural Features and Naive T Cell Frequency in Humans. 著者: Reiser, J.B. / Legoux, F. / Gras, S. / Trudel, E. / Chouquet, A. / Leger, A. / Le Gorrec, M. / Machillot, P. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
履歴 |
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-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 | 3mrl.cif.gz | 93.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3mrl.ent.gz | 69.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3mrl.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/mr/3mrl ftp://data.pdbj.org/pub/pdb/validation_reports/mr/3mrl | HTTPS FTP |
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-関連構造データ
-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: 34008.711 Da / 分子数: 1 / 断片: HLA-A*0201 alpha chain, UNP resiude 25-300 / 変異: A245V / 由来タイプ: 組換発現 詳細: C-terminal biotin acceptor peptide sequence tag (GSLHHILDAQKMVWNHR) 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA, HLA-A, HLAA / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): X90F LAQQ1 / 参照: UniProt: P01892, UniProt: P04439*PLUS |
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#2: タンパク質 | 分子量: 11879.356 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, BETA-2 MICROGLUBULIN, CDABP0092, HDCMA22P / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): X90F LAQQ1 / 参照: UniProt: P61769 |
#3: タンパク質・ペプチド | 分子量: 990.176 Da / 分子数: 1 / 断片: NS3 protein fragment, UNP residues 1073-1081 / 変異: C6V / 由来タイプ: 合成 詳細: chemical synthesis; Variant of a sequence occurring in Hepatitis C virus NS3 protein 由来: (合成) Hepatitis C virus genotype 1b (isolate HC-J1) (C型肝炎ウイルス) 参照: UniProt: Q03463 |
#4: 水 | ChemComp-HOH / |
-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: 2.43 Å3/Da / 溶媒含有率: 49.34 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 15% PEG 6000, 0.1M NaCitrate, 3.6mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: ID14-4 / 波長: 0.97569 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2006年11月11日 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 | 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: 0.97569 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 2.4→50 Å / Num. obs: 16618 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / 冗長度: 2.99 % / Biso Wilson estimate: 40.304 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.82 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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-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 3MRG 解像度: 2.41→15 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.871 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.585 / SU ML: 0.135 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.343 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. ...詳細: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. Rwork and Rfree values corresponds to the coordinates just before these very last cycles.
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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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 67.73 Å2 / Biso mean: 31.59 Å2 / Biso min: 9.16 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.41→15 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.409→2.47 Å / Total num. of bins used: 20
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