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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 4o9r | ||||||
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タイトル | Human Smoothened Receptor structure in complex with cyclopamine | ||||||
![]() | Smoothened homolog/Soluble cytochrome b562 chimeric protein | ||||||
![]() | SIGNALING PROTEIN / serial femtosecond crystallography / human SMO receptor / cyclopamine / novel protein engineering / GPCR network / PSI-Biology / free electron laser / Structural Genomics / membrane protein / XFEL / LCP / room temperature structure / GPCR / membrane | ||||||
機能・相同性 | ![]() ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / central nervous system neuron differentiation / 9+0 non-motile cilium / pancreas morphogenesis / regulation of somatic stem cell population maintenance / epithelial-mesenchymal cell signaling ...ventral midline determination / mesenchymal to epithelial transition involved in metanephric renal vesicle formation / regulation of heart morphogenesis / contact inhibition / negative regulation of hair follicle development / central nervous system neuron differentiation / 9+0 non-motile cilium / pancreas morphogenesis / regulation of somatic stem cell population maintenance / epithelial-mesenchymal cell signaling / myoblast migration / atrial septum morphogenesis / spinal cord dorsal/ventral patterning / determination of left/right asymmetry in lateral mesoderm / midgut development / left/right axis specification / ciliary tip / Activation of SMO / thalamus development / somite development / patched binding / forebrain morphogenesis / cellular response to cholesterol / type B pancreatic cell development / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of organ growth / BBSome-mediated cargo-targeting to cilium / dorsal/ventral neural tube patterning / smooth muscle tissue development / pattern specification process / cerebellar cortex morphogenesis / mammary gland epithelial cell differentiation / dentate gyrus development / dopaminergic neuron differentiation / commissural neuron axon guidance / oxysterol binding / positive regulation of multicellular organism growth / positive regulation of smoothened signaling pathway / Class B/2 (Secretin family receptors) / neural crest cell migration / cell fate specification / cAMP-dependent protein kinase inhibitor activity / anterior/posterior pattern specification / ciliary membrane / positive regulation of mesenchymal cell proliferation / negative regulation of epithelial cell differentiation / hair follicle morphogenesis / smoothened signaling pathway / positive regulation of neuroblast proliferation / heart looping / negative regulation of DNA binding / odontogenesis of dentin-containing tooth / protein kinase A catalytic subunit binding / endoplasmic reticulum-Golgi intermediate compartment / neuroblast proliferation / vasculogenesis / Hedgehog 'off' state / skeletal muscle fiber development / positive regulation of epithelial cell proliferation / homeostasis of number of cells within a tissue / epithelial cell proliferation / protein sequestering activity / centriole / astrocyte activation / negative regulation of protein phosphorylation / central nervous system development / G protein-coupled receptor activity / electron transport chain / Hedgehog 'on' state / multicellular organism growth / cilium / cerebral cortex development / positive regulation of protein import into nucleus / osteoblast differentiation / protein import into nucleus / endocytic vesicle membrane / late endosome / gene expression / in utero embryonic development / periplasmic space / electron transfer activity / protein stabilization / positive regulation of cell migration / iron ion binding / negative regulation of gene expression / intracellular membrane-bounded organelle / dendrite / heme binding / positive regulation of gene expression / negative regulation of apoptotic process / apoptotic process / negative regulation of transcription by RNA polymerase II / Golgi apparatus / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Wang, C. / Weierstall, U. / James, D. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C.H. / Doak, R.B. / Nelson, G. / Fromme, P. ...Wang, C. / Weierstall, U. / James, D. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C.H. / Doak, R.B. / Nelson, G. / Fromme, P. / Fromme, R. / Grotjohann, I. / Kupitz, C. / Zatsepin, N.A. / Liu, H. / Basu, S. / Wacker, D. / Han, G.W. / Katritch, V. / Boutet, S. / Messerschmidt, M. / Willams, G.J. / Koglin, J.E. / Seibert, M.M. / Klinker, M. / Gati, C. / Shoeman, R.L. / Barty, A. / Chapman, H.N. / Kirian, R.A. / Beyerlein, K.R. / Stevens, R.C. / Li, D. / Shah, S.T.A. / Howe, N. / Caffrey, M. / Cherezov, V. / GPCR Network (GPCR) | ||||||
![]() | ![]() タイトル: Lipidic cubic phase injector facilitates membrane protein serial femtosecond crystallography. 著者: Weierstall, U. / James, D. / Wang, C. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C. / Bruce Doak, R. / Nelson, G. / Fromme, P. / Fromme, R. / Grotjohann, I. / Kupitz, C. / Zatsepin, N.A. ...著者: Weierstall, U. / James, D. / Wang, C. / White, T.A. / Wang, D. / Liu, W. / Spence, J.C. / Bruce Doak, R. / Nelson, G. / Fromme, P. / Fromme, R. / Grotjohann, I. / Kupitz, C. / Zatsepin, N.A. / Liu, H. / Basu, S. / Wacker, D. / Han, G.W. / Katritch, V. / Boutet, S. / Messerschmidt, M. / Williams, G.J. / Koglin, J.E. / Marvin Seibert, M. / Klinker, M. / Gati, C. / Shoeman, R.L. / Barty, A. / Chapman, H.N. / Kirian, R.A. / Beyerlein, K.R. / Stevens, R.C. / Li, D. / Shah, S.T. / Howe, N. / Caffrey, M. / Cherezov, V. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 100.3 KB | 表示 | ![]() |
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PDB形式 | ![]() | 73.9 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 |
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-関連構造データ
関連構造データ | ![]() 4ib4S ![]() 4jkvS S: 精密化の開始モデル |
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類似構造データ | |
実験データセット #1 | データ参照: ![]() |
その他のデータベース |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
#1: タンパク質 | 分子量: 52395.199 Da / 分子数: 1 断片: UNP Q99835 residues 190-433, P0ABE7 residues 23-128, Q99835 residues 441-555 変異: M1007W, H1102I, R1106L / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() ![]() プラスミド: pFASTBAC 発現宿主: ![]() ![]() 株 (発現宿主): sf9 / 参照: UniProt: Q99835, UniProt: P0ABE7 |
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#2: 化合物 | ChemComp-CY8 / |
-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 3.16 Å3/Da / 溶媒含有率: 61.1 % |
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結晶化 | 温度: 293 K / 手法: 脂質キュービック相法 / pH: 7 詳細: 100 mM Hepes, 30 % (v/v) PEG 400, 100 mM NaCl , pH 7.0, Lipidic Cubic Phase (LCP), temperature 293K |
-データ収集
回折 | 平均測定温度: 294 K |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: Cornell-SLAC Pixel Array Detector (CSPAD) / 検出器: PIXEL / 日付: 2013年3月1日 |
放射 | モノクロメーター: K-B Mirrors / 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: 1.3 Å / 相対比: 1 |
反射 | 解像度: 3.2→40 Å / Num. obs: 10785 / % possible obs: 100 % |
反射 シェル | 解像度: 3.2→3.7 Å / % possible all: 100 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 4JKV for SMO and PDB ENTRY 4IB4 for BRIL 解像度: 3.204→39.325 Å / SU ML: 0.5 / σ(F): 1.38 / 位相誤差: 29.77 / 立体化学のターゲット値: ML
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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 | ||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 3.204→39.325 Å
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LS精密化 シェル |
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