+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4lcy | ||||||
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タイトル | Crystal structure of HLA-b46 at 1.6 angstrom resolution | ||||||
要素 |
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キーワード | MEMBRANE PROTEIN / antigen presenting / cell surface / HLA-B46 | ||||||
機能・相同性 | 機能・相同性情報 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / neutrophil degranulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / antigen processing and presentation of peptide antigen via MHC class I / regulation of T cell anergy / regulation of interleukin-6 production / type I interferon-mediated signaling pathway ...antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / neutrophil degranulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / antigen processing and presentation of peptide antigen via MHC class I / regulation of T cell anergy / regulation of interleukin-6 production / type I interferon-mediated signaling pathway / plasma membrane => GO:0005886 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / TAP binding / protection from natural killer cell mediated cytotoxicity / regulation of immune response / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / type II interferon-mediated signaling pathway / detection of bacterium / viral process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / 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 / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / viral capsid / Modulation by Mtb of host immune system / double-stranded RNA binding / 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 / nucleoside-triphosphate phosphatase / DAP12 signaling / MHC class II protein complex binding / protein complex oligomerization / early endosome membrane / late endosome membrane / monoatomic ion channel activity / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / protein homotetramerization / intracellular iron ion homeostasis / mRNA (nucleoside-2'-O-)-methyltransferase activity / adaptive immune response / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / amyloid fibril formation / learning or memory / RNA helicase activity 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Dengue virus 1 (デング熱ウイルス) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.6 Å | ||||||
データ登録者 | Liu, J.X. | ||||||
引用 | ジャーナル: To be Published タイトル: Crystal Structure Analysis of the Human Leukocyte Antigen B*46:01 著者: Liu, J.X. | ||||||
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 | 4lcy.cif.gz | 194.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4lcy.ent.gz | 152.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4lcy.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 | 4lcy_validation.pdf.gz | 453.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4lcy_full_validation.pdf.gz | 462.7 KB | 表示 | |
XML形式データ | 4lcy_validation.xml.gz | 42 KB | 表示 | |
CIF形式データ | 4lcy_validation.cif.gz | 64.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/lc/4lcy ftp://data.pdbj.org/pub/pdb/validation_reports/lc/4lcy | HTTPS FTP |
-関連構造データ
関連構造データ | 3c9nS 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: 31786.107 Da / 分子数: 2 / 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) / 株: B46:01 / 遺伝子: HLA, HLA-B, HLAB / プラスミド: pET30A / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P30484, UniProt: P01889*PLUS #2: タンパク質 | 分子量: 11879.356 Da / 分子数: 2 / 断片: UNP residues 21-119 / 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 MICROGLOBULIN, CDABP0092, HDCMA22P / プラスミド: pET30A / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: P61769 #3: タンパク質・ペプチド | 分子量: 1064.321 Da / 分子数: 2 / 由来タイプ: 合成 詳細: This sequence is one fragment of Dengue Virus 1 polyprotein. 由来: (合成) Dengue virus 1 (デング熱ウイルス) / 参照: UniProt: P17763*PLUS #4: 化合物 | ChemComp-NA / #5: 水 | ChemComp-HOH / | 配列の詳細 | THE SEQUENCE OF ENTITY 3 HAS IEDB ID 124151. | |
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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: 2.34 Å3/Da / 溶媒含有率: 47.54 % |
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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: 5.5 詳細: 0.1M BIS-TRIS pH 5.5, 25% POLYETHYLENE GLYCOL 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-データ収集
回折 | 平均測定温度: 298 K |
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放射光源 | 由来: シンクロトロン / サイト: NSRRC / ビームライン: BL13B1 / 波長: 1 Å |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年7月19日 |
放射 | モノクロメーター: GRAPHITE / 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 Å / 相対比: 1 |
反射 | 解像度: 1.6→25.2 Å / Num. all: 108570 / Num. obs: 107515 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 3.2 % / Rmerge(I) obs: 0.049 / Rsym value: 0.041 / Net I/σ(I): 12.8 |
反射 シェル | 解像度: 1.6→1.69 Å / 冗長度: 3.2 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 5.7 / Num. unique all: 15693 / % possible all: 99 |
-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: 3C9N 解像度: 1.6→25.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.309 / SU ML: 0.048 / 交差検証法: THROUGHOUT / σ(F): 2 / ESU R: 0.019 / ESU R Free: 0.019 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 18.109 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.6→25.2 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.6→1.641 Å / Total num. of bins used: 20
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