+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1tzh | ||||||
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タイトル | Crystal Structure of the Fab YADS1 Complexed with h-VEGF | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / phage display / antibody library / protein engineering (タンパク質工学) | ||||||
機能・相同性 | 機能・相同性情報 basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis ...basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / motor neuron migration / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / eye photoreceptor cell development / 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 / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of protein localization to early endosome / vascular wound healing / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / camera-type eye morphogenesis / positive regulation of epithelial tube formation / 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 / commissural neuron axon guidance / dopaminergic neuron differentiation / positive regulation of vascular permeability / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / cell migration involved in sprouting angiogenesis / extracellular matrix binding / retinal ganglion cell axon guidance / cardiac muscle cell development / 血管新生 / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / artery morphogenesis / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / chemoattractant activity / activation of protein kinase activity / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / positive regulation of cell division / macrophage differentiation / fibronectin binding / positive regulation of cell adhesion / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / 脈管形成 / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / 授乳 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell proliferation / 細胞外マトリックス / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / 分泌 / kidney development / cytokine activity / positive regulation of epithelial cell proliferation 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å | ||||||
データ登録者 | Fellouse, F.A. / Wiesmann, C. / Sidhu, S.S. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2004 タイトル: Synthetic antibodies from a four-amino-acid code: A dominant role for tyrosine in antigen recognition 著者: Fellouse, F.A. / Wiesmann, C. / Sidhu, S.S. #1: ジャーナル: J.Mol.Biol. / 年: 2004 タイトル: Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions 著者: Sidhu, S.S. / Li, B. / Chen, Y. / Fellouse, F.A. / Eigenbrot, C. / Fuh, G. | ||||||
履歴 |
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Remark 999 | SEQUENCE THE AUTHORS INFORMED THAT THE SEQUENCES OF Fab YADS1 Light Chain and Fab YADS1 heavy Chain ...SEQUENCE THE AUTHORS INFORMED THAT THE SEQUENCES OF Fab YADS1 Light Chain and Fab YADS1 heavy Chain are not yet available in any reference sequence database. |
-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 | 1tzh.cif.gz | 210.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1tzh.ent.gz | 169.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1tzh.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/tz/1tzh ftp://data.pdbj.org/pub/pdb/validation_reports/tz/1tzh | 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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単位格子 |
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詳細 | For VEGF, the biological assembly is chain V and W, linked by a disulfide bridge. For the Fab VEGF complex, the biological assembly is all chains. |
-要素
#1: タンパク質 | 分子量: 11948.680 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: VEGF, VEGFA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P15692 #2: 抗体 | 分子量: 23035.486 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: F / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): 16C9 #3: 抗体 | 分子量: 24300.898 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: F / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): 16C9 #4: 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: 2.8 Å3/Da / 溶媒含有率: 56 % |
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結晶化 | 温度: 292 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: PEG 3350, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-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: ALS / ビームライン: 5.0.2 / 波長: 1 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2003年5月6日 |
放射 | モノクロメーター: Double-crystal, 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: 1 Å / 相対比: 1 |
反射 | 解像度: 2.6→50 Å / Num. all: 41883 / Num. obs: 41828 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 3.7 % / Biso Wilson estimate: 54.378 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 16.8 |
反射 シェル | 解像度: 2.6→2.69 Å / 冗長度: 3.5 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4162 / Rsym value: 0.423 / % possible all: 99.1 |
-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: The VEGF from pdb entry 1VPF. The Fab from an in-house determined structure. 解像度: 2.6→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.721 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.595 / ESU R Free: 0.325 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 25.123 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.6→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.6→2.655 Å / Total num. of bins used: 25
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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