+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ktl | ||||||
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タイトル | The human non-classical major histocompatibility complex molecule HLA-E | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / HLA-E (HLA-E) / MHC / NON-CLASSICAL MHC / HLA / BETA 2 MICROGLOBULIN (Β2-ミクログロブリン) | ||||||
機能・相同性 | 機能・相同性情報 : / : / retina homeostasis / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production ...: / : / retina homeostasis / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / 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 / positive regulation of interleukin-4 production / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / sensory perception of smell / positive regulation of tumor necrosis factor production / 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 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 / defense response to Gram-positive bacterium / 免疫応答 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / RIGID-BODY REFINEMENT OF 1KPR / 解像度: 3.1 Å | ||||||
データ登録者 | Holmes, M.A. / Strong, R.K. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2003 タイトル: HLA-E allelic variants: Correlating differential expression, peptide affinities, crystal structures and thermal stabilities 著者: Strong, R.K. / Holmes, M.A. / Li, P. / Braun-Jones, L. / Lee, N. / Geraghty, D.E. | ||||||
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 | 1ktl.cif.gz | 151.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ktl.ent.gz | 121.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ktl.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/kt/1ktl ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1ktl | 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: 31511.596 Da / 分子数: 2 / 変異: R107G / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-E / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): UBS / 参照: UniProt: P13747 #2: タンパク質 | 分子量: 11879.356 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XA90 / 参照: UniProt: P01884, UniProt: P61769*PLUS #3: タンパク質・ペプチド | 分子量: 984.213 Da / 分子数: 2 / 由来タイプ: 合成 #4: 化合物 | ChemComp-SO4 / | |
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-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: 4.52 Å3/Da / 溶媒含有率: 72.78 % | ||||||||||||||||||||||||
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 詳細: ammonium sulfate, PEG 400, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K, pH 8.00 | ||||||||||||||||||||||||
結晶化 | *PLUS 温度: 22 ℃ / pH: 8 / 手法: 蒸気拡散法 | ||||||||||||||||||||||||
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 | 由来: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.5418 |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 1999年7月12日 / 詳細: 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: 3.1→25 Å / Num. all: 27568 / Num. obs: 27568 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / 冗長度: 9.6 % / Biso Wilson estimate: 85.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.4 |
反射 シェル | 解像度: 3.1→3.15 Å / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1230 / % possible all: 84.1 |
反射 | *PLUS 最高解像度: 3.1 Å / 最低解像度: 25 Å / Num. measured all: 265243 |
反射 シェル | *PLUS 最高解像度: 3.1 Å / % possible obs: 84.1 % |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: RIGID-BODY REFINEMENT OF 1KPR 開始モデル: PDB ENTRY 1KPR 解像度: 3.1→25 Å / Isotropic thermal model: ISOTROPIC GROUP B'S / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: ENGH & HUBER
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原子変位パラメータ | Biso mean: 63 Å2 | |||||||||||||||||||||||||
Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 3.1→25 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3.1→3.21 Å
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精密化 | *PLUS 最高解像度: 3.1 Å / 最低解像度: 25 Å / Rfactor Rfree: 0.28 | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS
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