+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2v7d | ||||||
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タイトル | 14-3-3 protein zeta in complex with Thr758 phosphorylated integrin beta2 peptide | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / MEMBRANE (生体膜) / INTEGRIN (インテグリン) / RECEPTOR (受容体) / CYTOPLASM (細胞質) / ACETYLATION (アセチル化) / TRANSMEMBRANE (膜貫通型タンパク質) / BETA2 INTEGRIN / PHOSPHORYLATION (リン酸化) / DISEASE MUTATION / PYRROLIDONE CARBOXYLIC ACID (ピログルタミン酸) / 14-3-3 ZETA / GLYCOPROTEIN (糖タンパク質) / CELL ADHESION (細胞接着) | ||||||
機能・相同性 | 機能・相同性情報 KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / synaptic target recognition / integrin alphaX-beta2 complex / : / cellular extravasation ...KSRP (KHSRP) binds and destabilizes mRNA / RHO GTPases activate PKNs / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / synaptic target recognition / integrin alphaX-beta2 complex / : / cellular extravasation / GP1b-IX-V activation signalling / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / Deactivation of the beta-catenin transactivating complex / respiratory system process / neutrophil degranulation / : / Rap1 signalling / TP53 Regulates Metabolic Genes / complement component C3b binding / regulation of programmed cell death / Interleukin-3, Interleukin-5 and GM-CSF signaling / neutrophil migration / Toll Like Receptor 4 (TLR4) Cascade / leukocyte migration involved in inflammatory response / negative regulation of dopamine metabolic process / tube formation / cell-cell adhesion via plasma-membrane adhesion molecules / natural killer cell activation / heterotypic cell-cell adhesion / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / cell adhesion mediated by integrin / toll-like receptor 4 signaling pathway / phagocytosis, engulfment / leukocyte cell-cell adhesion / leukocyte migration / receptor clustering / amyloid-beta clearance / endodermal cell differentiation / plasma membrane raft / tertiary granule membrane / ficolin-1-rich granule membrane / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / phosphoserine residue binding / protein targeting / endothelial cell migration / regulation of immune response / Integrin cell surface interactions / specific granule membrane / regulation of peptidyl-tyrosine phosphorylation / ERK1 and ERK2 cascade / heat shock protein binding / hippocampal mossy fiber to CA3 synapse / cell adhesion molecule binding / extracellular matrix organization / receptor-mediated endocytosis / cell-matrix adhesion / 好中球 / regulation of ERK1 and ERK2 cascade / protein sequestering activity / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / lung development / microglial cell activation / receptor internalization / 細胞接着 / cytokine-mediated signaling pathway / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / extracellular vesicle / 遊走 / メラノソーム / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of cell shape / 血管新生 / Interleukin-4 and Interleukin-13 signaling / receptor complex / 細胞接着 / 炎症 / protein domain specific binding / external side of plasma membrane / protein phosphorylation / focal adhesion / apoptotic process / Neutrophil degranulation / protein kinase binding / negative regulation of transcription by RNA polymerase II / 細胞膜 / シグナル伝達 / extracellular exosome 類似検索 - 分子機能 | ||||||
生物種 | BOS TAURUS (ウシ) HOMO SAPIENS (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å | ||||||
データ登録者 | Takala, H. / Ylanne, J. | ||||||
引用 | ジャーナル: Blood / 年: 2008 タイトル: Beta2 Integrin Phosphorylation on Thr758 Acts as a Molecular Switch to Regulate 14-3-3 and Filamin Binding. 著者: Takala, H. / Nurminen, E. / Nurmi, S.M. / Aatonen, M. / Strandin, T. / Takatalo, M. / Kiema, T. / Gahmberg, C.G. / Ylanne, J. / Fagerholm, S.C. | ||||||
履歴 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-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 | 2v7d.cif.gz | 195.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2v7d.ent.gz | 157.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2v7d.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/v7/2v7d ftp://data.pdbj.org/pub/pdb/validation_reports/v7/2v7d | 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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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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-要素
#1: タンパク質 | 分子量: 27921.221 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) BOS TAURUS (ウシ) / プラスミド: PET-15B / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P63103 #2: タンパク質・ペプチド | 分子量: 1130.186 Da / 分子数: 4 / Fragment: INTEGRIN CYTOPLASMIC TAIL, RESIDUES 755-764 / 由来タイプ: 合成 / 詳細: THR758 SIDE CHAIN PHOSPHORYLATED / 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: Q53HS5, UniProt: P05107*PLUS #3: 水 | ChemComp-HOH / | 構成要素の詳細 | ADAPTER PROTEIN IMPLICATED IN THE REGULATION OF A LARGE SPECTRUM OF BOTH GENERAL AND SPECIALIZED ...ADAPTER PROTEIN IMPLICATED | 配列の詳細 | RESIDUES (-1-0) ARE REMNANTS OF A FUSION PROTEIN AND A PART OF ONLY THIS STRUCTURE | |
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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: 2.84 Å3/Da / 溶媒含有率: 56.32 % / 解説: NONE |
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結晶化 | pH: 8.5 詳細: 18-19% PEG3350, 10MM CACL2, 1MM NICL2, 100MM TRIS PH8.5 |
-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: ESRF / ビームライン: ID14-3 / 波長: 0.931 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2007年3月17日 / 詳細: TOROIDAL MIRROR |
放射 | モノクロメーター: DIAMOND (111), GE(220) / 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: 0.931 Å / 相対比: 1 |
反射 | 解像度: 2.5→500.1 Å / Num. obs: 40994 / % possible obs: 99.9 % / 冗長度: 9 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.09 / Net I/σ(I): 16.86 |
反射 シェル | 解像度: 2.5→2.59 Å / 冗長度: 8.94 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 4.91 / Rsym value: 0.534 / % possible all: 99.9 |
-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 1A4O 解像度: 2.5→47.6 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINTS / 交差検証法: THROUGHOUT / σ(F): 0 立体化学のターゲット値: LEAST SQUARES RESIDUAL FOR HEMIHEDRAL TWINNING 詳細: USED TWINNING FRACTION 0.306. TWINNING OPERATOR H,-H-K,-L
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 80.04 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 65.1 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.5→47.6 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.5→2.59 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP_TPO4.PARAM / Topol file: PROTEIN_TPO3.TOP |