+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2erf | ||||||
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タイトル | Crystal Structure of the Thrombospondin-1 N-terminal Domain at 1.45A Resolution | ||||||
要素 | Thrombospondin-1Thrombospondin 1 | ||||||
キーワード | SUGAR BINDING PROTEIN / Thrombospondin-1 / TSP-1 / N-terminal TSPN / HBD | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins ...negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / collagen V binding / negative regulation of dendritic cell antigen processing and presentation / negative regulation of nitric oxide mediated signal transduction / chronic inflammatory response / negative regulation of sprouting angiogenesis / negative regulation of endothelial cell chemotaxis / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / positive regulation of transforming growth factor beta1 production / negative regulation of fibroblast growth factor receptor signaling pathway / negative regulation of long-chain fatty acid import across plasma membrane / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / engulfment of apoptotic cell / low-density lipoprotein particle binding / negative regulation of focal adhesion assembly / fibrinogen complex / peptide cross-linking / positive regulation of chemotaxis / fibrinogen binding / Signaling by PDGF / Α顆粒 / negative regulation of interleukin-12 production / negative regulation of cell migration involved in sprouting angiogenesis / positive regulation of macrophage activation / negative regulation of plasminogen activation / transforming growth factor beta binding / positive regulation of endothelial cell apoptotic process / positive regulation of fibroblast migration / 血管新生 / proteoglycan binding / negative regulation of endothelial cell migration / extracellular matrix structural constituent / Syndecan interactions / endopeptidase inhibitor activity / negative regulation of cell-matrix adhesion / phosphatidylserine binding / positive regulation of macrophage chemotaxis / negative regulation of cGMP-mediated signaling / response to testosterone / fibroblast growth factor binding / behavioral response to pain / positive regulation of transforming growth factor beta receptor signaling pathway / negative regulation of endothelial cell proliferation / response to magnesium ion / negative regulation of blood vessel endothelial cell migration / fibronectin binding / response to unfolded protein / positive regulation of blood vessel endothelial cell migration / Integrin cell surface interactions / laminin binding / positive regulation of blood coagulation / negative regulation of fibrinolysis / response to glucose / response to mechanical stimulus / positive regulation of phosphorylation / response to endoplasmic reticulum stress / negative regulation of angiogenesis / 細胞外マトリックス / positive regulation of endothelial cell migration / positive regulation of translation / platelet alpha granule lumen / 筋小胞体 / response to progesterone / 分泌 / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of smooth muscle cell proliferation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / positive regulation of MAP kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cellular response to growth factor stimulus / response to calcium ion / positive regulation of angiogenesis / positive regulation of reactive oxygen species metabolic process / 遊走 / integrin binding / positive regulation of tumor necrosis factor production / Platelet degranulation / cellular response to heat / heparin binding / cellular response to tumor necrosis factor / collagen-containing extracellular matrix / protease binding / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 細胞接着 / positive regulation of cell migration / 免疫応答 / response to xenobiotic stimulus / 炎症 / negative regulation of cell population proliferation / external side of plasma membrane / 小胞体 / apoptotic process / calcium ion binding / positive regulation of cell population proliferation / negative regulation of apoptotic process / 細胞膜 / 小胞体 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.45 Å | ||||||
データ登録者 | Tan, K. / Wang, J. / Lawler, J. | ||||||
引用 | ジャーナル: Structure / 年: 2006 タイトル: The structures of the thrombospondin-1 N-terminal domain and its complex with a synthetic pentameric heparin. 著者: Tan, K. / Duquette, M. / Liu, J.H. / Zhang, R. / Joachimiak, A. / Wang, J.H. / Lawler, J. | ||||||
履歴 |
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Remark 999 | SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: ...SEQUENCE THE SEQUENCE OF THE WHOLE CONSTRUCT IS LISTED HERE: RSPWNRIPESGGDNSVFDIFELTGAARKGSGRRLVKGPDPSSPAFRIEDA NLIPPVPDDKFQDLVDAVRTEKGFLLLASLRQMKKTRGTLLALERKDHSG QVFSVVSNGKAGTLDLSLTVQGKQHVVSVEEALLATGQWKSITLFVQEDR AQLYIDCEKMENAELDVPIQSVFTRDLASIARLRIAKGGVNDNFQGVLQN VRFVFGTTPEDILRNKGCSSSTSVLLTLDNNVVNGSSPAIRTNTGHHHHHH THE PURIFIED PROTEIN WAS TREATED WITH CHYMOTRYPSIN AND RE-PURIFIED BEFORE CRYSTALLIZATION. THE EXACT N-TERMINAL OR C-TERMINAL SEQUENCES ARE NOT KNOWN. THE SEQRES REPRESENTS THE RESIDUES IN THE COORDINATES. |
-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 | 2erf.cif.gz | 100.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2erf.ent.gz | 76.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2erf.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/er/2erf ftp://data.pdbj.org/pub/pdb/validation_reports/er/2erf | 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: 22901.035 Da / 分子数: 1 / 断片: N-terminal Domain / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: THBS1, TSP, TSP1 / 細胞株 (発現宿主): S2 Cell 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P07996 |
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#2: 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: 2.2 Å3/Da / 溶媒含有率: 42.7 % |
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結晶化 | 温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.6 詳細: 30% PEG1500 and 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-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: APS / ビームライン: 19-ID / 波長: 1.00931 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2005年7月7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: 1.00931 Å / 相対比: 1 |
反射 | 解像度: 1.45→30 Å / Num. all: 34155 / Num. obs: 34155 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.8 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 39.7 |
反射 シェル | 解像度: 1.45→1.5 Å / 冗長度: 2.3 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2422 / % possible all: 68.7 |
-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 ENTRY 1Z78 解像度: 1.45→22.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.702 / SU ML: 0.048 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.08 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
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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: 25.962 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.45→22.86 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.45→1.488 Å / Total num. of bins used: 20
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