+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5hgh | ||||||
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タイトル | HLA*A2402 complexed with HIV nef138 10mer epitope | ||||||
要素 |
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キーワード | IMMUNE SYSTEM / HLA / Antigen presentation / HIV | ||||||
機能・相同性 | 機能・相同性情報 Nef mediated downregulation of CD28 cell surface expression / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / Nef and signal transduction / Nef Mediated CD4 Down-regulation / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target ...Nef mediated downregulation of CD28 cell surface expression / Late Phase of HIV Life Cycle / Nef Mediated CD8 Down-regulation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / suppression by virus of host autophagy / Nef and signal transduction / Nef Mediated CD4 Down-regulation / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / Uncoating of the HIV Virion / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / host cell Golgi membrane / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / Binding and entry of HIV virion / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / virion component / cellular response to iron(III) ion / Assembly Of The HIV Virion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / Budding and maturation of HIV virion / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / SH3 domain binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / positive regulation of type II interferon production / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / 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 / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / antibacterial humoral response / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Human immunodeficiency virus type 1 (ヒト免疫不全ウイルス) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2.392 Å | ||||||
データ登録者 | Shi, Y. / Qi, J. / Gao, G.F. | ||||||
引用 | ジャーナル: Cell Rep / 年: 2016 タイトル: Effects of a Single Escape Mutation on T Cell and HIV-1 Co-adaptation. 著者: Sun, X. / Shi, Y. / Akahoshi, T. / Fujiwara, M. / Gatanaga, H. / Schonbach, C. / Kuse, N. / Appay, V. / Gao, G.F. / Oka, S. / Takiguchi, M. | ||||||
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 | 5hgh.cif.gz | 97.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5hgh.ent.gz | 72.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5hgh.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
文書・要旨 | 5hgh_validation.pdf.gz | 439 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5hgh_full_validation.pdf.gz | 442.9 KB | 表示 | |
XML形式データ | 5hgh_validation.xml.gz | 18.4 KB | 表示 | |
CIF形式データ | 5hgh_validation.cif.gz | 26.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/hg/5hgh ftp://data.pdbj.org/pub/pdb/validation_reports/hg/5hgh | HTTPS FTP |
-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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 31683.086 Da / 分子数: 1 / 断片: UNP RESIDUES 25-298 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-A, HLAA 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P05534, 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, CDABP0092, HDCMA22P 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: P61769 |
#3: タンパク質・ペプチド | 分子量: 1290.511 Da / 分子数: 1 / 断片: UNP RESIDUES 135-144 / 由来タイプ: 合成 由来: (合成) Human immunodeficiency virus type 1 (ヒト免疫不全ウイルス) 参照: UniProt: P18801, UniProt: P04601*PLUS |
#4: 水 | ChemComp-HOH / |
Has protein modification | Y |
-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 2.96 Å3/Da / 溶媒含有率: 58.4 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 0.1 M MES monohydrate pH 6.5, 12% w/v Polyethylene glycol 20000 |
-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 MICROMAX-007 HF / 波長: 1.54178 Å |
検出器 | タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2009年3月5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: 1.54178 Å / 相対比: 1 |
反射 | 解像度: 2.392→50 Å / Num. obs: 20191 / % possible obs: 97.2 % / 冗長度: 4.1 % / Net I/σ(I): 19.968 |
反射 シェル | 解像度: 2.392→2.49 Å / 冗長度: 3.6 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.642 / % possible all: 92.6 |
-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: 2BCK 解像度: 2.392→42.706 Å / SU ML: 0.37 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 23.95 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 39.01 Å2 / ksol: 0.352 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 2.392→42.706 Å
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拘束条件 |
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LS精密化 シェル |
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