+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1b0r | ||||||
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タイトル | CRYSTAL STRUCTURE OF HLA-A*0201 COMPLEXED WITH A PEPTIDE WITH THE CARBOXYL-TERMINAL GROUP SUBSTITUTED BY A METHYL GROUP | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / HLA-A2 / ANTIGENIC PEPTIDES / CLASS I MHC MOLECULES / HLA-A2 COMPLEXES / HYDROGEN BONDS (水素結合) / PROTEIN STRUCTURE (タンパク質構造) | ||||||
機能・相同性 | 機能・相同性情報 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 ...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 / 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 / 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 / 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 / E3 ubiquitin ligases ubiquitinate target proteins / 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 / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / 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 / endoplasmic reticulum membrane / 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: 2.9 Å | ||||||
データ登録者 | Bouvier, M. / Guo, H. / Smith, K.J. / Wiley, D.C. | ||||||
引用 | ジャーナル: Proteins / 年: 1998 タイトル: Crystal structures of HLA-A*0201 complexed with antigenic peptides with either the amino- or carboxyl-terminal group substituted by a methyl group. 著者: Bouvier, M. / Guo, H.C. / Smith, K.J. / Wiley, D.C. | ||||||
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 | 1b0r.cif.gz | 88 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1b0r.ent.gz | 66.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1b0r.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/b0/1b0r ftp://data.pdbj.org/pub/pdb/validation_reports/b0/1b0r | HTTPS FTP |
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-関連構造データ
関連構造データ | 1hhiS 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: 31854.203 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAINS ALPHA 1,ALPHA 2 AND ALPHA 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞内の位置: EXTRACELLULARGlossary of biology / プラスミド: PHN1 / 細胞内の位置 (発現宿主): INCLUSION BODIES / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XA90 / 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 / 断片: BETA 2 MICROGLOBULIN / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞内の位置: EXTRACELLULARGlossary of biology / プラスミド: PHN1 / 細胞内の位置 (発現宿主): INCLUSION BODIES / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XA90 / 参照: UniProt: P61769 |
#3: タンパク質・ペプチド | 分子量: 922.164 Da / 分子数: 1 / Mutation: NON / 由来タイプ: 合成 / 詳細: MATRIX PEPTIDE |
-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: 2.51 Å3/Da / 溶媒含有率: 50.96 % | ||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 6.5 / 詳細: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 | ||||||||||||||||||||||||||||||||||||||||
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 | 波長: 1.5418 |
検出器 | タイプ: MAR scanner 180 mm plate / 検出器: IMAGE PLATE |
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: 2.9→15 Å / Num. obs: 9323 / % possible obs: 89 % / Observed criterion σ(I): -3 / 冗長度: 4.3 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.9 |
反射 シェル | 解像度: 2.9→3 Å / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 6 / % possible all: 92 |
反射 シェル | *PLUS % possible obs: 92 % |
-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: 1HHI 解像度: 2.9→6 Å / Rfactor Rfree error: 0.011 / 交差検証法: THROUGHOUT / σ(F): 2
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原子変位パラメータ | Biso mean: 15.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.9→6 Å
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拘束条件 |
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Xplor file |
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS 最高解像度: 2.9 Å / 最低解像度: 3.03 Å / Rfactor Rfree: 0.424 / Rfactor Rwork: 0.36 |