+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6p7j | ||||||
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タイトル | Crystal structure of Latency Associated Peptide unbound to TGF-beta1 | ||||||
要素 | Transforming growth factor beta-1 proprotein | ||||||
キーワード | CYTOKINE (サイトカイン) / pro-domain / latency / cancer (悪性腫瘍) / transforming | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / embryonic liver development / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / odontoblast differentiation / connective tissue replacement involved in inflammatory response wound healing / positive regulation of receptor signaling pathway via STAT / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / membrane protein intracellular domain proteolysis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / heart valve morphogenesis / positive regulation of vasculature development / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / receptor catabolic process / positive regulation of extracellular matrix assembly / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / negative regulation of biomineral tissue development / cell-cell junction organization / negative regulation of myoblast differentiation / positive regulation of vascular permeability / deubiquitinase activator activity / positive regulation of endothelial cell apoptotic process / response to cholesterol / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / negative regulation of protein localization to plasma membrane / 血管新生 / neural tube development / Molecules associated with elastic fibres / RUNX3 regulates CDKN1A transcription / positive regulation of epidermal growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / negative regulation of fat cell differentiation / macrophage derived foam cell differentiation / Syndecan interactions / negative regulation of cell-cell adhesion / positive regulation of interleukin-17 production / negative regulation of blood vessel endothelial cell migration / TGF-beta receptor signaling activates SMADs / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / RUNX3 regulates p14-ARF / positive regulation of cell division / cellular response to low-density lipoprotein particle stimulus / negative regulation of cell cycle / ECM proteoglycans / positive regulation of vascular endothelial growth factor production / 上皮間葉転換 / positive regulation of collagen biosynthetic process / positive regulation of epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / lymph node development / 脈管形成 / chondrocyte differentiation / hematopoietic progenitor cell differentiation / salivary gland morphogenesis / regulation of cell migration / extrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / cellular response to transforming growth factor beta stimulus / antigen binding / 細胞外マトリックス / positive regulation of protein metabolic process / protein export from nucleus / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / positive regulation of superoxide anion generation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / negative regulation of miRNA transcription / negative regulation of protein phosphorylation / platelet alpha granule lumen / response to progesterone / cytokine activity / neural tube closure / positive regulation of protein secretion / positive regulation of protein-containing complex assembly 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: 3.501 Å | ||||||
データ登録者 | Stachowski, T.R. / Snell, M.E. / Snell, E.H. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Iucrj / 年: 2020 タイトル: Structural insights into conformational switching in latency-associated peptide between transforming growth factor beta-1 bound and unbound states 著者: Stachowski, T.R. / Snell, M.E. / Snell, E.H. | ||||||
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 | 6p7j.cif.gz | 48.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6p7j.ent.gz | 32 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6p7j.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/p7/6p7j ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7j | HTTPS FTP |
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-関連構造データ
関連構造データ | 5vqpS 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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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 29274.240 Da / 分子数: 1 / 変異: R249A / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TGFB1, TGFB / プラスミド: pTT3 / Cell (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P01137 |
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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: 2.03 Å3/Da / 溶媒含有率: 39.42 % |
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結晶化 | 温度: 293 K / 手法: batch mode / pH: 4.6 詳細: Reservoir composition: 20% PEG3350, 300 mM NaAc pH 4.6 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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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: 17-ID / 波長: 1 Å | ||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2018年11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: 3.5→36.31 Å / Num. obs: 3332 / % possible obs: 99.6 % / 冗長度: 3.7 % / CC1/2: 0.899 / Rmerge(I) obs: 0.345 / Rpim(I) all: 0.209 / Rrim(I) all: 0.406 / Net I/σ(I): 3.1 / Num. measured all: 12411 / Scaling rejects: 46 | ||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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-位相決定
位相決定 | 手法: 分子置換 |
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-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: 5VQP 解像度: 3.501→36.31 Å / SU ML: 0.49 / 交差検証法: THROUGHOUT / 位相誤差: 24.54
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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 | ||||||||||||||||||
原子変位パラメータ | Biso max: 224.46 Å2 / Biso mean: 111.1007 Å2 / Biso min: 40.77 Å2 | ||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 3.501→36.31 Å
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LS精密化 シェル | 解像度: 3.501→3.625 Å / Rfactor Rfree error: 0
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