+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5irn | ||||||
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タイトル | Crystal structure of rabbit NOD2 in an ADP-bound state (Crystal form1) | ||||||
要素 | Uncharacterized protein | ||||||
キーワード | IMMUNE SYSTEM (免疫系) / NOD2 / innate immunity (自然免疫系) | ||||||
機能・相同性 | 機能・相同性情報 biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / host-mediated regulation of intestinal microbiota composition / positive regulation of dendritic cell antigen processing and presentation / intestinal stem cell homeostasis ...biosynthetic process of antibacterial peptides active against Gram-positive bacteria / detection of muramyl dipeptide / muramyl dipeptide binding / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / negative regulation of T cell mediated immunity / regulation of neutrophil chemotaxis / negative regulation of interleukin-18 production / host-mediated regulation of intestinal microbiota composition / positive regulation of dendritic cell antigen processing and presentation / intestinal stem cell homeostasis / negative regulation of toll-like receptor 2 signaling pathway / regulation of appetite / toll-like receptor 2 signaling pathway / negative regulation of macrophage cytokine production / negative regulation of macrophage apoptotic process / positive regulation of humoral immune response mediated by circulating immunoglobulin / antibacterial innate immune response / maintenance of gastrointestinal epithelium / positive regulation of mitophagy / positive regulation of xenophagy / xenophagy / positive regulation of B cell activation / positive regulation of type 2 immune response / positive regulation of protein K63-linked ubiquitination / cellular response to muramyl dipeptide / CARD domain binding / cellular response to peptidoglycan / negative regulation of interleukin-12 production / peptidoglycan binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of cytokine production involved in inflammatory response / positive regulation of monocyte chemotactic protein-1 production / positive regulation of macrophage cytokine production / pattern recognition receptor activity / negative regulation of interleukin-2 production / temperature homeostasis / extrinsic component of plasma membrane / positive regulation of Notch signaling pathway / response to exogenous dsRNA / positive regulation of interleukin-17 production / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interleukin-10 production / response to muramyl dipeptide / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / 食作用 / detection of bacterium / positive regulation of phagocytosis / JNK cascade / negative regulation of inflammatory response to antigenic stimulus / phagocytic vesicle / Hsp70 protein binding / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / response to endoplasmic reticulum stress / innate immune response in mucosa / ubiquitin binding / positive regulation of interleukin-1 beta production / establishment of localization in cell / positive regulation of epithelial cell proliferation / positive regulation of interleukin-8 production / positive regulation of JNK cascade / Hsp90 protein binding / ADP binding / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of peptidyl-tyrosine phosphorylation / actin binding / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / 獲得免疫系 / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / 細胞骨格 / defense response to bacterium / protein-containing complex binding / protein kinase binding / ゴルジ体 / 細胞膜 / positive regulation of transcription by RNA polymerase II / protein-containing complex / ミトコンドリア / ATP binding / 細胞質基質 類似検索 - 分子機能 | ||||||
生物種 | Oryctolagus cuniculus (ウサギ) | ||||||
手法 | X線回折 / シンクロトロン / 解像度: 2.34 Å | ||||||
データ登録者 | Maekawa, S. / Ohto, U. / Shimizu, T. | ||||||
引用 | ジャーナル: Nat Commun / 年: 2016 タイトル: Crystal structure of NOD2 and its implications in human disease. 著者: Maekawa, S. / Ohto, U. / Shibata, T. / Miyake, K. / Shimizu, T. | ||||||
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 | 5irn.cif.gz | 305.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5irn.ent.gz | 244.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5irn.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/ir/5irn ftp://data.pdbj.org/pub/pdb/validation_reports/ir/5irn | 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: 91878.695 Da / 分子数: 1 / 断片: UNP RESIDUES 194-1020 / 由来タイプ: 組換発現 / 由来: (組換発現) Oryctolagus cuniculus (ウサギ) / 遺伝子: NOD2 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: G1T469 |
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#2: 化合物 | ChemComp-ADP / |
#3: 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: 4.25 Å3/Da / 溶媒含有率: 71.09 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 5% PEG 20000, 5% MPD, 100 mM Hepes pH 7.8, 500 mM NaCl |
-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: シンクロトロン / サイト: SPring-8 / ビームライン: BL41XU / 波長: 1 Å |
検出器 | タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2014年10月11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 Å / 相対比: 1 |
反射 | 解像度: 2.3→92.7 Å / Num. obs: 57510 / % possible obs: 92.6 % / 冗長度: 6.7 % / Net I/σ(I): 29.7 |
-解析
ソフトウェア |
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精密化 | 解像度: 2.34→92.7 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 12.943 / SU ML: 0.135 / 交差検証法: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.185 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 76.976 Å2
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精密化ステップ | サイクル: 1 / 解像度: 2.34→92.7 Å
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拘束条件 |
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