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基本情報
登録情報 | データベース: EMDB / ID: EMD-8472 | |||||||||
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タイトル | MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution | |||||||||
![]() | Complex between monomeric TGF-b and its receptor, TbRII | |||||||||
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![]() | TRANSFERASE | |||||||||
機能・相同性 | ![]() regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / ascending aorta morphogenesis / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / uterine wall breakdown ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / ascending aorta morphogenesis / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / uterine wall breakdown / bronchus morphogenesis / cardioblast differentiation / mammary gland morphogenesis / lens fiber cell apoptotic process / positive regulation of timing of catagen / growth plate cartilage chondrocyte growth / positive regulation of cardioblast differentiation / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / activin receptor activity / positive regulation of heart contraction / cardiac right ventricle morphogenesis / miRNA transport / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / regulation of transforming growth factor beta2 production / Langerhans cell differentiation / atrial septum morphogenesis / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / signaling / transforming growth factor beta receptor activity / secondary palate development / cardiac left ventricle morphogenesis / glial cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / somatic stem cell division / heart valve morphogenesis / endocardial cushion fusion / positive regulation of T cell tolerance induction / atrial septum primum morphogenesis / membranous septum morphogenesis / lung lobe morphogenesis / positive regulation of integrin biosynthetic process / positive regulation of NK T cell differentiation / cardiac epithelial to mesenchymal transition / eye development / cranial skeletal system development / neural retina development / positive regulation of stress-activated MAPK cascade / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / receptor protein serine/threonine kinase / pulmonary valve morphogenesis / transmembrane receptor protein serine/threonine kinase activity / activin binding / type I transforming growth factor beta receptor binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / SMAD protein signal transduction / regulation of stem cell differentiation / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / glycosaminoglycan binding / kinase activator activity / embryonic cranial skeleton morphogenesis / negative regulation of Ras protein signal transduction / transforming growth factor beta binding / response to cholesterol / aortic valve morphogenesis / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / embryo development ending in birth or egg hatching / odontogenesis / dopamine biosynthetic process / lens development in camera-type eye / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / trachea formation / artery morphogenesis / endocardial cushion morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / hair follicle morphogenesis / generation of neurons / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / activation of protein kinase activity 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 電子線結晶学 / クライオ電子顕微鏡法 / 解像度: 2.9 Å | |||||||||
![]() | Weiss SC / de la Cruz MJ | |||||||||
![]() | ![]() タイトル: Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED. 著者: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P ...著者: M Jason de la Cruz / Johan Hattne / Dan Shi / Paul Seidler / Jose Rodriguez / Francis E Reyes / Michael R Sawaya / Duilio Cascio / Simon C Weiss / Sun Kyung Kim / Cynthia S Hinck / Andrew P Hinck / Guillermo Calero / David Eisenberg / Tamir Gonen / ![]() 要旨: Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from ...Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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マップデータ | ![]() | 604.4 KB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 14.7 KB 14.7 KB | 表示 表示 | ![]() |
画像 | ![]() | 372.9 KB | ||
Filedesc metadata | ![]() | 5.4 KB | ||
Filedesc structureFactors | ![]() | 955.4 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 476.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 475.8 KB | 表示 | |
XML形式データ | ![]() | 4.1 KB | 表示 | |
CIF形式データ | ![]() | 4.5 KB | 表示 | |
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-関連構造データ
関連構造データ | ![]() 5ty4MC ![]() 8216C ![]() 8217C ![]() 8218C ![]() 8219C ![]() 8220C ![]() 8221C ![]() 8222C ![]() 5k7nC ![]() 5k7oC ![]() 5k7pC ![]() 5k7qC ![]() 5k7rC ![]() 5k7sC ![]() 5k7tC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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類似構造データ |
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EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Complex between monomeric TGF-b and its receptor, TbRII | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X: 0.94386 Å / Y: 0.93855 Å / Z: 0.94653 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
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試料の構成要素
-全体 : Complex between monomeric TGF-b and its receptor, TbRII
全体 | 名称: Complex between monomeric TGF-b and its receptor, TbRII |
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要素 |
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-超分子 #1: Complex between monomeric TGF-b and its receptor, TbRII
超分子 | 名称: Complex between monomeric TGF-b and its receptor, TbRII タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 19.072 KDa |
-分子 #1: TGF-beta receptor type-2
分子 | 名称: TGF-beta receptor type-2 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: receptor protein serine/threonine kinase |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 11.788519 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: FPQLCKFCDV RFSTCDNQKS CMSNCSITSI CEKPQEVCVA VWRKNDENIT LETVCHDPKL PYHDFILEDA ASPTCIMKEK KKPGETFFM CSCSSDECND NIIF UniProtKB: TGF-beta receptor type-2 |
-分子 #2: mmTGF-b2-7m
分子 | 名称: mmTGF-b2-7m / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 11.076813 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: CCLRPLYIDF RKDLGWKWIH EPKGYNANFC AGACPYLWSS DTQHSRVLSL YNTINPEASA SPCCVSQDLE PLTIVYYVGR KPKVEQLSN MIVKSCKC |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 電子線結晶学 |
試料の集合状態 | 3D array |
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試料調製
緩衝液 | pH: 7.5 / 構成要素 - 濃度: 100.0 mM / 構成要素 - 名称: HEPES |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TECNAI F20 |
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撮影 | フィルム・検出器のモデル: TVIPS TEMCAM-F416 (4k x 4k) デジタル化 - サイズ - 横: 2048 pixel / デジタル化 - サイズ - 縦: 2048 pixel / 撮影したグリッド数: 2 / 実像数: 353 / 回折像の数: 353 / 平均露光時間: 4.1 sec. / 平均電子線量: 0.004 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: DIFFRACTION / カメラ長: 2000 mm |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Tecnai F20 / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
精密化 | 空間: RECIPROCAL / プロトコル: OTHER |
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得られたモデル | ![]() PDB-5ty4: |