+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 7t1l | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Crystal structure of a superbinder Fes SH2 domain (sFesS) in complex with a high affinity phosphopeptide | ||||||||||||
![]() |
| ||||||||||||
![]() | SIGNALING PROTEIN / Src Homology 2 (SH2) / superbinder / rational engineering | ||||||||||||
機能・相同性 | ![]() terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / positive regulation of myeloid cell differentiation / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking ...terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / positive regulation of myeloid cell differentiation / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization / negative regulation of p38MAPK cascade / Netrin-1 signaling / cortical microtubule organization / uropod / regulation of mast cell degranulation / astral microtubule organization / postsynaptic actin cytoskeleton organization / positive regulation of protein localization to early endosome / regulation of vesicle-mediated transport / cellular response to vitamin D / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / filopodium assembly / CRMPs in Sema3A signaling / positive regulation of multicellular organism growth / microtubule bundle formation / protein-containing complex localization / positive regulation of monocyte differentiation / regulation of cell motility / establishment of endothelial barrier / sphingosine-1-phosphate receptor signaling pathway / S100 protein binding / Sensory processing of sound by outer hair cells of the cochlea / centrosome cycle / Sensory processing of sound by inner hair cells of the cochlea / myoblast proliferation / cardiac muscle cell proliferation / protein kinase A binding / microvillus membrane / negative regulation of T cell receptor signaling pathway / leukocyte cell-cell adhesion / negative regulation of interleukin-2 production / cortical cytoskeleton / regulation of cell differentiation / protein kinase A regulatory subunit binding / plasma membrane raft / protein kinase A catalytic subunit binding / Recycling pathway of L1 / brush border / microvillus / actin filament bundle assembly / Sema3A PAK dependent Axon repulsion / immunological synapse / regulation of cell adhesion / immunoglobulin receptor binding / cellular response to cAMP / positive regulation of microtubule polymerization / ruffle / cell adhesion molecule binding / protein kinase A signaling / phosphatidylinositol binding / ciliary basal body / filopodium / protein localization to plasma membrane / cell projection / cell periphery / actin filament / positive regulation of protein localization to plasma membrane / adherens junction / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / Signaling by SCF-KIT / receptor internalization / cytoplasmic side of plasma membrane / negative regulation of ERK1 and ERK2 cascade / fibrillar center / ruffle membrane / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / positive regulation of protein catabolic process / chemotaxis / microtubule cytoskeleton / disordered domain specific binding / actin filament binding / actin cytoskeleton / apical part of cell / actin binding / regulation of cell population proliferation / regulation of cell shape / ATPase binding / actin cytoskeleton organization / cytoplasmic vesicle / microtubule binding / basolateral plasma membrane / protein tyrosine kinase activity / vesicle / protein autophosphorylation / cell adhesion / endosome / cadherin binding 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||
![]() | Martyn, G.D. / Singer, A.U. / Veggiani, G. / Kurinov, I. / Sicheri, F. / Sidhu, S.S. | ||||||||||||
資金援助 | ![]()
| ||||||||||||
![]() | ![]() タイトル: Engineered SH2 Domains for Targeted Phosphoproteomics. 著者: Martyn, G.D. / Veggiani, G. / Kusebauch, U. / Morrone, S.R. / Yates, B.P. / Singer, A.U. / Tong, J. / Manczyk, N. / Gish, G. / Sun, Z. / Kurinov, I. / Sicheri, F. / Moran, M.F. / Moritz, R.L. / Sidhu, S.S. | ||||||||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 157.1 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 111.4 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
---|
-関連構造データ
関連構造データ | ![]() 7t1kC ![]() 7t1uC ![]() 3bkbS S: 精密化の開始モデル C: 同じ文献を引用 ( |
---|---|
類似構造データ | 類似検索 - 機能・相同性 ![]() |
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
単位格子 |
|
-
要素
#1: タンパク質 | 分子量: 11201.869 Da / 分子数: 2 / 断片: SH2 domain 変異: Residues 486 to 492 mutated from QGKQEYV to ETVKGAYA, and I505L (Uniprot numbering) 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() 参照: UniProt: P07332, non-specific protein-tyrosine kinase #2: タンパク質・ペプチド | 分子量: 879.888 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) ![]() #3: 化合物 | ChemComp-NA / | #4: 化合物 | ChemComp-CL / | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
---|
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 1.87 Å3/Da / 溶媒含有率: 34.35 % |
---|---|
結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8.5 詳細: 1.3 M Sodium Citrate Tribasic Dihydrate and 100 mM Bis-Tris Propane (pH=8.5) Temp details: Room temperature |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年7月19日 / 詳細: mirrors |
放射 | モノクロメーター: Si(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: 0.97918 Å / 相対比: 1 |
反射 | 解像度: 1.3→43.32 Å / Num. obs: 45098 / % possible obs: 99.4 % / 冗長度: 6.4 % / Biso Wilson estimate: 17.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12 |
反射 シェル | 解像度: 1.3→1.32 Å / 冗長度: 6.6 % / Rmerge(I) obs: 0.758 / Num. unique obs: 2269 / CC1/2: 0.723 / % possible all: 98.6 |
-
解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]() 開始モデル: 3BKB 解像度: 1.35→43.32 Å / SU ML: 0.1474 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 19.7741 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 22.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.35→43.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
|