+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1m1x | |||||||||
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タイトル | CRYSTAL STRUCTURE OF THE EXTRACELLULAR SEGMENT OF INTEGRIN ALPHA VBETA3 BOUND TO MN2+ | |||||||||
要素 |
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キーワード | CELL ADHESION / GENU / HYBRID DOMAIN / BETA-TAIL DOMAIN / PSI DOMAIN / EGF DOMAIN / MIDAS / ADMIDAS / CAGE MOTIF / PROPELLER / A-DOMAIN / THIGH DOMAIN / CALF DOMAIN | |||||||||
機能・相同性 | 機能・相同性情報 integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding ...integrin alphav-beta6 complex / integrin alphav-beta8 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / : / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / 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 / Laminin interactions / 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 / entry into host cell by a symbiont-containing vacuole / 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 / regulation of phagocytosis / 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 / transforming growth factor beta binding / platelet-derived growth factor receptor binding / filopodium membrane / positive regulation of small GTPase mediated signal transduction / 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 intracellular signal transduction / 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 / endodermal cell differentiation / 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 / positive regulation of cell adhesion / ECM proteoglycans / voltage-gated calcium channel activity / positive regulation of T cell migration / positive regulation of bone resorption / vasculogenesis / Integrin cell surface interactions / coreceptor activity / specific granule membrane / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / extrinsic apoptotic signaling pathway in absence of ligand / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / embryo implantation / phagocytic vesicle / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading 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 / フーリエ合成 / 解像度: 3.3 Å | |||||||||
データ登録者 | Xiong, J.-P. / Stehle, T. / Zhang, R. / Joachimiak, A. / Frech, M. / Goodman, S.L. / Arnaout, M.A. | |||||||||
引用 | ジャーナル: Science / 年: 2002 タイトル: Crystal structure of the extracellular segment of integrin alpha Vbeta3 in complex with an Arg-Gly-Asp ligand. 著者: Xiong, J.P. / Stehle, T. / Zhang, R. / Joachimiak, A. / Frech, M. / Goodman, S.L. / Arnaout, M.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 | 1m1x.cif.gz | 299.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1m1x.ent.gz | 241.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1m1x.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 | 1m1x_validation.pdf.gz | 807.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1m1x_full_validation.pdf.gz | 880.9 KB | 表示 | |
XML形式データ | 1m1x_validation.xml.gz | 39.1 KB | 表示 | |
CIF形式データ | 1m1x_validation.cif.gz | 56.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/m1/1m1x ftp://data.pdbj.org/pub/pdb/validation_reports/m1/1m1x | 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
-タンパク質 , 2種, 2分子 AB
#1: タンパク質 | 分子量: 105880.164 Da / 分子数: 1 / 断片: RESIDUES 31-987 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: SF9 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: GenBank: 14743192, UniProt: P06756*PLUS |
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#2: タンパク質 | 分子量: 76650.305 Da / 分子数: 1 / 断片: RESIDUES 27-718 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: SF9 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P05106 |
-糖 , 3種, 11分子
#3: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #4: 多糖 | #5: 糖 | ChemComp-NAG / |
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-非ポリマー , 1種, 6分子
#6: 化合物 | ChemComp-MN / |
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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: 4.17 Å3/Da / 溶媒含有率: 70.51 % |
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結晶化 | 温度: 278 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6 詳細: PEG, MES, Mn, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-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: 1.0332 Å |
検出器 | タイプ: CUSTOM-MADE / 検出器: CCD / 日付: 2001年6月24日 |
放射 | モノクロメーター: UNDULATOR / 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: 1.0332 Å / 相対比: 1 |
反射 | 解像度: 3.3→50 Å / Num. all: 47393 / Num. obs: 44739 / % possible obs: 94.4 % / Observed criterion σ(I): -3 |
反射 シェル | 解像度: 3.3→3.4 Å / % possible all: 86.1 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: フーリエ合成 / 解像度: 3.3→20 Å / σ(F): 2 / 立体化学のターゲット値: Engh & Huber
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精密化ステップ | サイクル: LAST / 解像度: 3.3→20 Å
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拘束条件 |
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