+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2bpd | ||||||
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タイトル | STRUCTURE OF MURINE DECTIN-1 | ||||||
要素 | DECTIN-1CLEC7A | ||||||
キーワード | RECEPTOR (受容体) / DECTIN-1 / BETA-GLUCAN (Β-グルカン) / FUNGAL RECOGNITION / C-TYPE LECTIN-LIKE DOMAIN / CTLD / CARBOHYDRATE (炭水化物) | ||||||
機能・相同性 | 機能・相同性情報 (1->3)-beta-D-glucan immune receptor activity / positive regulation of lymphocyte activation / detection of yeast / detection of molecule of fungal origin / (1->3)-beta-D-glucan binding / cell recognition / detection of fungus / regulation of calcineurin-NFAT signaling cascade / response to molecule of fungal origin / positive regulation of dendritic cell cytokine production ...(1->3)-beta-D-glucan immune receptor activity / positive regulation of lymphocyte activation / detection of yeast / detection of molecule of fungal origin / (1->3)-beta-D-glucan binding / cell recognition / detection of fungus / regulation of calcineurin-NFAT signaling cascade / response to molecule of fungal origin / positive regulation of dendritic cell cytokine production / cell surface pattern recognition receptor signaling pathway / positive regulation of cell maturation / positive regulation of cytokine production involved in immune response / antifungal innate immune response / opsonin binding / positive regulation of interleukin-23 production / positive regulation of stress-activated MAPK cascade / CLEC7A (Dectin-1) signaling / response to yeast / leukocyte activation involved in immune response / cell activation / phagocytosis, recognition / positive regulation of killing of cells of another organism / cellular response to molecule of fungal origin / positive regulation of T-helper 17 type immune response / positive regulation of cytokine production involved in inflammatory response / positive regulation of monocyte chemotactic protein-1 production / regulation of canonical NF-kappaB signal transduction / pattern recognition receptor activity / phagocytosis, engulfment / polysaccharide binding / positive regulation of wound healing / positive regulation of respiratory burst / stimulatory C-type lectin receptor signaling pathway / positive regulation of interleukin-10 production / positive regulation of calcium-mediated signaling / positive regulation of phagocytosis / positive regulation of interleukin-2 production / positive regulation of interleukin-12 production / positive regulation of superoxide anion generation / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of protein-containing complex assembly / positive regulation of DNA-binding transcription factor activity / 細胞接着 / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / 炎症 / external side of plasma membrane / 自然免疫系 / positive regulation of cell population proliferation / positive regulation of gene expression / 細胞膜 / identical protein binding / metal ion binding / 細胞膜 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | MUS MUSCULUS (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.5 Å | ||||||
データ登録者 | Brown, J. / O'Callaghan, C.A. / Marshall, A.S.J. / Gilbert, R.J.C. / Siebold, C. / Gordon, S. / Brown, G.D. / Jones, E.Y. | ||||||
引用 | ジャーナル: Protein Sci. / 年: 2007 タイトル: Structure of the Fungal Beta-Glucan-Binding Immune Receptor Dectin-1: Implications for Function. 著者: Brown, J. / O'Callaghan, C.A. / Marshall, A.S.J. / Gilbert, R.J.C. / Siebold, C. / Gordon, S. / Brown, G.D. / Jones, E.Y. | ||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-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 | 2bpd.cif.gz | 76.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2bpd.ent.gz | 56.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2bpd.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/bp/2bpd ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bpd | 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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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 117 - 243 / Label seq-ID: 15 - 141
NCS oper: (Code: given Matrix: (-0.99887, 0.02025, -0.04306), ベクター: |
-要素
#1: タンパク質 | 分子量: 16329.065 Da / 分子数: 2 断片: EXTRACELLULAR BETA-GLUCAN RECOGNITION DOMAIN, RESIDUES 113-244 由来タイプ: 組換発現 / 由来: (組換発現) MUS MUSCULUS (ハツカネズミ) / 細胞株: RAW264.7 / プラスミド: PET22B / 発現宿主: ESCHERICHIA COLI BL21(DE3) (大腸菌) / Variant (発現宿主): Rosetta / 参照: UniProt: Q6QLQ4 #2: 水 | ChemComp-HOH / | |
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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: 2.14 Å3/Da / 溶媒含有率: 42.42 % 解説: MOLECULAR REPLACEMENT USED THE CASPR WEBSERVER WITH 6 STARTING MODELS. STRUCTURAL ALIGNMENT OF STARTING MODELS WAS USED TO GENERATE HOMOLOGY MODELS AND POLY-ALA MODELS TO BE USED IN THE ...解説: MOLECULAR REPLACEMENT USED THE CASPR WEBSERVER WITH 6 STARTING MODELS. STRUCTURAL ALIGNMENT OF STARTING MODELS WAS USED TO GENERATE HOMOLOGY MODELS AND POLY-ALA MODELS TO BE USED IN THE MOLECULAR REPLACEMENT SEARCH. |
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結晶化 | 詳細: 0.2 M DI-AMMONIUM HYDROGEN CITRATE, 20% PEG 3350 |
-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: ESRF / ビームライン: ID14-2 / 波長: 0.933 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2004年6月19日 / 詳細: TOROIDAL MIRROR |
放射 | モノクロメーター: DIAMOND (111), GE(220) / 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: 0.933 Å / 相対比: 1 |
反射 | 解像度: 1.5→30 Å / Num. obs: 41593 / % possible obs: 97 % / Observed criterion σ(I): -3 / 冗長度: 4.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.1 |
反射 シェル | 解像度: 1.5→1.55 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.7 / % possible all: 78.1 |
-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: PDB ENTRIES 1K9J, 1FM5, 1HQ8, 1JA3, 1MPU, 1E87 解像度: 1.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.23 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.105 / 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: 30.53 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.5→30 Å
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拘束条件 |
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