+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1m6o | ||||||
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タイトル | Crystal Structure of HLA B*4402 in complex with HLA DPA*0201 peptide | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / MHC I / GLYCOPROTEIN (糖タンパク質) | ||||||
機能・相同性 | 機能・相同性情報 : / : / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / TAP binding ...: / : / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of interleukin-12 production / regulation of dendritic cell differentiation / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / regulation of membrane depolarization / 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 / 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 / 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 / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / 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 / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / 獲得免疫系 / learning or memory / endosome membrane / defense response to Gram-positive bacterium / 免疫応答 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / 小胞体 / ゴルジ体 / signaling receptor binding / focal adhesion / 自然免疫系 / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / ゴルジ体 / 細胞膜 / 小胞体 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.6 Å | ||||||
データ登録者 | Macdonald, W.A. / Purcell, A.W. / Williams, D.S. / Mifsud, N.A. / Ely, L.K. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Brooks, A.G. ...Macdonald, W.A. / Purcell, A.W. / Williams, D.S. / Mifsud, N.A. / Ely, L.K. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Brooks, A.G. / Lovrecz, G.O. / Lu, L. / Rossjohn, J. / McCluskey, J. | ||||||
引用 | ジャーナル: J.Exp.Med. / 年: 2003 タイトル: A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition. 著者: Macdonald, W.A. / Purcell, A.W. / Mifsud, N.A. / Ely, L.K. / Williams, D.S. / Chang, L. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Burrows, S.R. / Tait, B.D. / ...著者: Macdonald, W.A. / Purcell, A.W. / Mifsud, N.A. / Ely, L.K. / Williams, D.S. / Chang, L. / Gorman, J.J. / Clements, C.S. / Kjer-Nielsen, L. / Koelle, D.M. / Burrows, S.R. / Tait, B.D. / Holdsworth, R. / Brooks, A.G. / Lovrecz, G.O. / Lu, L. / Rossjohn, J. / McCluskey, J. | ||||||
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 | 1m6o.cif.gz | 102 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1m6o.ent.gz | 81.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1m6o.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/m6/1m6o ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6o | 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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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 31980.258 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: Truncated heavy chain / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pET / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P30481, UniProt: P01889*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: pET / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21 (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P01884, UniProt: P61769*PLUS |
#3: タンパク質・ペプチド | 分子量: 1090.165 Da / 分子数: 1 / 由来タイプ: 合成 詳細: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN homo sapiens. It was derived from the HLA DP alpha (DPA*0201) polypeptide chain. 参照: GenBank: 14602923, UniProt: Q95HB9*PLUS |
#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: 2.55 Å3/Da / 溶媒含有率: 51.78 % | ||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.2 詳細: 20-30% PEG 4K, 0.1M citrate, 0.2M ammonium acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: Macdonald, W., (2002) FEBS Lett., 527, 27. / PH range low: 5.9 / PH range high: 5.2 | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: 回転陽極 / タイプ: RIGAKU / 波長: 1.5418 Å |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 詳細: OSMIC mirrors |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.6→50 Å / Num. obs: 59302 / % possible obs: 96.8 % / 冗長度: 4.76 % / Rmerge(I) obs: 0.049 |
反射 シェル | 最高解像度: 1.6 Å / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2 |
反射 | *PLUS 冗長度: 4.8 % / Num. measured all: 282153 |
反射 シェル | *PLUS % possible obs: 92.7 % |
-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: 1.6→50 Å /
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精密化ステップ | サイクル: LAST / 解像度: 1.6→50 Å
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拘束条件 |
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拘束条件 | *PLUS
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