+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4o3u | ||||||
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タイトル | Zymogen HGF-beta/MET with Zymogen Activator Peptide ZAP2.3 | ||||||
要素 |
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キーワード | transferase/growth factor / trypsin homoloy / receptor activation / transferase-growth factor complex | ||||||
機能・相同性 | 機能・相同性情報 regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / negative regulation of guanyl-nucleotide exchange factor activity / hepatocyte growth factor receptor activity / Drug-mediated inhibition of MET activation / skeletal muscle cell proliferation / endothelial cell morphogenesis / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / MET interacts with TNS proteins / MET Receptor Activation / semaphorin-plexin signaling pathway involved in axon guidance / hepatocyte growth factor receptor signaling pathway / semaphorin receptor activity / MET receptor recycling / semaphorin receptor complex / pancreas development / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / Sema4D mediated inhibition of cell attachment and migration / MET activates PI3K/AKT signaling / negative regulation of stress fiber assembly / positive regulation of endothelial cell chemotaxis / negative regulation of Rho protein signal transduction / MET activates PTK2 signaling / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / branching morphogenesis of an epithelial tube / positive chemotaxis / negative regulation of thrombin-activated receptor signaling pathway / chemoattractant activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / semaphorin-plexin signaling pathway / epithelial to mesenchymal transition / establishment of skin barrier / positive regulation of osteoblast differentiation / MET activates RAS signaling / phagocytosis / MECP2 regulates neuronal receptors and channels / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of microtubule polymerization / Interleukin-7 signaling / negative regulation of autophagy / basal plasma membrane / cell chemotaxis / InlB-mediated entry of Listeria monocytogenes into host cell / platelet alpha granule lumen / liver development / epithelial cell proliferation / molecular function activator activity / growth factor activity / cell morphogenesis / neuron differentiation / Negative regulation of MET activity / receptor protein-tyrosine kinase / negative regulation of inflammatory response / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / Platelet degranulation / PIP3 activates AKT signaling / nervous system development / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein phosphatase binding / protein tyrosine kinase activity / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor complex / positive regulation of cell migration / positive regulation of protein phosphorylation / phosphorylation / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / ATP binding / identical protein binding / membrane / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) synthetic (人工物) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.04 Å | ||||||
データ登録者 | Eigenbrot, C. / Landgraf, K.E. / Steffek, M. | ||||||
引用 | ジャーナル: Nat.Chem.Biol. / 年: 2014 タイトル: An allosteric switch for pro-HGF/Met signaling using zymogen activator peptides. 著者: Landgraf, K.E. / Steffek, M. / Quan, C. / Tom, J. / Yu, C. / Santell, L. / Maun, H.R. / Eigenbrot, C. / Lazarus, R.A. | ||||||
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 | 4o3u.cif.gz | 158.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4o3u.ent.gz | 122.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4o3u.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 | 4o3u_validation.pdf.gz | 446.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4o3u_full_validation.pdf.gz | 457.9 KB | 表示 | |
XML形式データ | 4o3u_validation.xml.gz | 26.6 KB | 表示 | |
CIF形式データ | 4o3u_validation.cif.gz | 35.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/o3/4o3u ftp://data.pdbj.org/pub/pdb/validation_reports/o3/4o3u | HTTPS FTP |
-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: 26800.920 Da / 分子数: 1 / 断片: HGF-beta (UNP Residues 25-567) / 変異: V495G/C604S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HGF, HPTA 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P14210 |
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#2: タンパク質 | 分子量: 62714.141 Da / 分子数: 1 / 断片: Sema-PSI (UNP Residues 496-728) / 変異: L303K/V304R/P305K/R306K/G307R / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MET 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P08581, receptor protein-tyrosine kinase |
#3: タンパク質・ペプチド | 分子量: 1786.081 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: synthetic peptide library displayed on phage / 由来: (合成) synthetic (人工物) |
-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: 3.44 Å3/Da / 溶媒含有率: 64.26 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.2 詳細: 8% PEG8000, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-データ収集
回折 | 平均測定温度: 110 K |
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放射光源 | 由来: シンクロトロン / サイト: SSRL / ビームライン: BL12-2 / 波長: 0.9794 Å |
検出器 | タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2012年5月23日 |
放射 | モノクロメーター: Si(111) / 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: 0.9794 Å / 相対比: 1 |
反射 | 解像度: 3.04→34.76 Å / Num. all: 24419 / Num. obs: 24340 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 6.6 % / Biso Wilson estimate: 102.77 Å2 / Rsym value: 0.056 / Net I/σ(I): 23 |
-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 1SHY 解像度: 3.04→34.76 Å / Cor.coef. Fo:Fc: 0.8969 / Cor.coef. Fo:Fc free: 0.8574 / SU R Cruickshank DPI: 1.39 / Isotropic thermal model: individual atom isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ | Biso mean: 94.12 Å2
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Refine analyze | Luzzati coordinate error obs: 0.593 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.04→34.76 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 3.04→3.17 Å / Total num. of bins used: 12
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