+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1qty | ||||||
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タイトル | VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR | ||||||
要素 |
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キーワード | HORMONE/GROWTH FACTOR RECEPTOR / COMPLEX (GROWTH FACTOR-RECEPTOR) / FLT-1 / VEGF RECEPTOR / RECEPTOR TYROSINE KINASE / CYSTINE KNOT / GLYCOPROTEIN / IMMUNOGLOBULIN-LIKE DOMAIN / I-SET / HORMONE-GROWTH FACTOR RECEPTOR complex | ||||||
機能・相同性 | 機能・相同性情報 vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / hyaloid vascular plexus regression / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor binding / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / vascular wound healing / positive regulation of protein localization to early endosome / regulation of hematopoietic progenitor cell differentiation / vascular endothelial growth factor receptor activity / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / embryonic morphogenesis / camera-type eye morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / platelet-derived growth factor receptor binding / surfactant homeostasis / negative regulation of epithelial to mesenchymal transition / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / blood vessel morphogenesis / negative regulation of vascular endothelial cell proliferation / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / branching involved in blood vessel morphogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / monocyte chemotaxis / growth factor binding / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / positive regulation of osteoblast differentiation 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING / 解像度: 2.7 Å | ||||||
データ登録者 | Wiesmann, C. / de Vos, A.M. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 1999 タイトル: Solution structure of the VEGF-binding domain of Flt-1: comparison of its free and bound states. 著者: Starovasnik, M.A. / Christinger, H.W. / Wiesmann, C. / Champe, M.A. / de Vos, A.M. / Skelton, N.J. #1: ジャーナル: Cell(Cambridge,Mass.) / 年: 1997 タイトル: Crystal Structure at 1.7 A Resolution of Vegf in Complex with Domain 2 of the Flt-1 Receptor 著者: Wiesmann, C. / Fuh, G. / Christinger, H.W. / Eigenbrot, C. / Wells, J.A. / de Vos, A.M. | ||||||
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 | 1qty.cif.gz | 159.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1qty.ent.gz | 128.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1qty.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/qt/1qty ftp://data.pdbj.org/pub/pdb/validation_reports/qt/1qty | 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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2 |
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3 |
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単位格子 |
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詳細 | CHAINS V, W, X, and Y FORM A BIOLOGICALLY ACTIVE COMPLEX. CHAINS R, S, T, and U FORM A BIOLOGICALLY ACTIVE COMPLEX. |
-要素
#1: タンパク質 | 分子量: 11948.680 Da / 分子数: 4 / 断片: RECEPTOR BINDING DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P15692 #2: タンパク質 | 分子量: 11538.298 Da / 分子数: 4 / 断片: DOMAIN 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P17948 |
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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: 2.36 Å3/Da / 溶媒含有率: 47.89 % | ||||||||||||||||||||||||||||||||||||||||||
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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: 8.5 詳細: PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 詳細: Wiesmann, C., (1997) Cell, 91, 695. | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: 回転陽極 / タイプ: RIGAKU / 波長: 1.5418 |
検出器 | タイプ: MARRESEARCH / 検出器: AREA DETECTOR / 日付: 1996年12月24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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.7→30 Å / Num. all: 24216 / Num. obs: 24098 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.7 % / Rsym value: 0.049 / Net I/σ(I): 13.3 |
反射 シェル | 解像度: 2.7→2.76 Å / 冗長度: 3 % / Num. unique all: 1544 / Rsym value: 0.311 / % possible all: 98 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: MOLECULAR REPLACEMENT IN COMBINATION WITH MULTI-CRYSTAL AVERAGING 開始モデル: 1VPF 解像度: 2.7→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / 交差検証法: FREE R / σ(F): 0.2 / 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: 63.5 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.7→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.7→2.82 Å / Total num. of bins used: 8
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ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.851 / 分類: refinement | ||||||||||||||||||||||||||||
精密化 | *PLUS | ||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.4 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.383 |