+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1tye | |||||||||
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タイトル | Structural basis for allostery in integrins and binding of ligand-mimetic therapeutics to the platelet receptor for fibrinogen | |||||||||
要素 |
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キーワード | CELL ADHESION / crystal structure / platelet integrin alphaIIBbeta3 / fibrinogen binding / allostery / therapeutic antagonism | |||||||||
機能・相同性 | 機能・相同性情報 tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / ruffle membrane / VEGFA-VEGFR2 Pathway / cell-cell adhesion / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / regulation of protein localization 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: 2.9 Å | |||||||||
データ登録者 | Xiao, T. / Takagi, J. / Coller, B.S. / Wang, J.-H. / Springer, T.A. | |||||||||
引用 | ジャーナル: Nature / 年: 2004 タイトル: Structural basis for allostery in integrins and binding to fibrinogen-mimetic therapeutics 著者: Xiao, T. / Takagi, J. / Coller, B.S. / Wang, J.-H. / Springer, T.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 | 1tye.cif.gz | 532.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1tye.ent.gz | 431.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1tye.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 | 1tye_validation.pdf.gz | 1.4 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1tye_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 1tye_validation.xml.gz | 100.5 KB | 表示 | |
CIF形式データ | 1tye_validation.cif.gz | 134.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ty/1tye ftp://data.pdbj.org/pub/pdb/validation_reports/ty/1tye | HTTPS FTP |
-関連構造データ
関連構造データ | 1tvxS 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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2 |
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3 |
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単位格子 |
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-要素
-タンパク質 , 2種, 6分子 ACEBDF
#1: タンパク質 | 分子量: 49044.395 Da / 分子数: 3 / 断片: residues 1-452 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGAB / Cell (発現宿主): Hampster Ovary cells 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 株 (発現宿主): Lec 3.2.8.1 / 参照: UniProt: P08514 #2: タンパク質 | 分子量: 48719.242 Da / 分子数: 3 / 断片: residues 1-440 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGAB / Cell (発現宿主): Hampster Ovary cells 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 株 (発現宿主): Lec 3.2.8.1 / 参照: UniProt: P05106 |
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-糖 , 3種, 10分子
#3: 多糖 | #4: 多糖 | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #6: 糖 | ChemComp-NAG / |
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-非ポリマー , 4種, 144分子
#5: 化合物 | ChemComp-CA / #7: 化合物 | #8: 化合物 | #9: 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: 4.8 Å3/Da / 溶媒含有率: 74 % |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7 詳細: 10% PEG 8000, 0.4 M magnesium acetate, 0.1 M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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: CHESS / ビームライン: A1 / 波長: 0.976 Å |
検出器 | タイプ: ADSC QUANTUM 210 / 検出器: CCD / 日付: 2003年10月4日 / 詳細: mirror |
放射 | モノクロメーター: Rh-coated SI / 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: 0.976 Å / 相対比: 1 |
反射 | 解像度: 2.9→50 Å / Num. all: 123653 / Num. obs: 121498 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 10 % / Biso Wilson estimate: 74.5 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 17.4 |
反射 シェル | 解像度: 2.9→3 Å / 冗長度: 6 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 3 / Num. unique all: 11567 / Rsym value: 0.602 / % possible all: 93.9 |
-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 1TVX 解像度: 2.9→50 Å / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 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: 63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.416 Å | |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.9→50 Å
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拘束条件 |
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