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基本情報
登録情報 | データベース: PDB / ID: 8xm7 | ||||||||||||
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タイトル | Cryo-EM structure of the RhoG/DOCK5/ELMO1/Rac1 complex: RhoG/DOCK5/ELMO1 focused map | ||||||||||||
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![]() | SIGNALING PROTEIN / ELMO / DOCK / GEF / GTPASE / RHO / RAC | ||||||||||||
機能・相同性 | ![]() negative regulation of vascular associated smooth muscle contraction / regulation of ruffle assembly / podosome assembly / engulfment of apoptotic cell / guanyl-nucleotide exchange factor complex / cortical cytoskeleton organization / bone remodeling / myoblast fusion / Nef and signal transduction / activation of GTPase activity ...negative regulation of vascular associated smooth muscle contraction / regulation of ruffle assembly / podosome assembly / engulfment of apoptotic cell / guanyl-nucleotide exchange factor complex / cortical cytoskeleton organization / bone remodeling / myoblast fusion / Nef and signal transduction / activation of GTPase activity / positive regulation of vascular associated smooth muscle cell migration / podosome / RHO GTPases activate KTN1 / motor neuron axon guidance / anchoring junction / establishment or maintenance of cell polarity / phagocytosis, engulfment / positive regulation of epithelial cell migration / Rac protein signal transduction / Rho protein signal transduction / RHOG GTPase cycle / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / GPVI-mediated activation cascade / RAC1 GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / cell chemotaxis / secretory granule membrane / cell projection / cell motility / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / actin filament organization / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / small GTPase binding / VEGFA-VEGFR2 Pathway / SH3 domain binding / Constitutive Signaling by Aberrant PI3K in Cancer / cell migration / PIP3 activates AKT signaling / Factors involved in megakaryocyte development and platelet production / regulation of cell shape / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / actin cytoskeleton organization / cytoskeleton / focal adhesion / GTPase activity / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / protein kinase binding / positive regulation of DNA-templated transcription / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.91 Å | ||||||||||||
![]() | Kukimoto-Niino, M. / Katsura, K. / Ishizuka-Katsura, Y. / Mishima-Tsumagari, C. / Yonemochi, M. / Inoue, M. / Nakagawa, R. / Kaushik, R. / Zhang, K.Y.J. / Shirouzu, M. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: RhoG facilitates a conformational transition in the guanine nucleotide exchange factor complex DOCK5/ELMO1 to an open state. 著者: Mutsuko Kukimoto-Niino / Kazushige Katsura / Yoshiko Ishizuka-Katsura / Chiemi Mishima-Tsumagari / Mayumi Yonemochi / Mio Inoue / Reiko Nakagawa / Rahul Kaushik / Kam Y J Zhang / Mikako Shirouzu / ![]() 要旨: The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK- ...The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK-Rac pathway during engulfment and migration. Recent cryo-EM structures of the DOCK2/ELMO1 and DOCK2/ELMO1/Rac1 complexes have identified closed and open conformations that are key to understanding the autoinhibition mechanism. Nevertheless, the structural details of RhoG-mediated activation of the DOCK/ELMO complex remain elusive. Herein, we present cryo-EM structures of DOCK5/ELMO1 alone and in complex with RhoG and Rac1. The DOCK5/ELMO1 structure exhibits a closed conformation similar to that of DOCK2/ELMO1, suggesting a shared regulatory mechanism of the autoinhibitory state across DOCK-A/B subfamilies (DOCK1-5). Conversely, the RhoG/DOCK5/ELMO1/Rac1 complex adopts an open conformation that differs from that of the DOCK2/ELMO1/Rac1 complex, with RhoG binding to both ELMO1 and DOCK5. The alignment of the DOCK5 phosphatidylinositol (3,4,5)-trisphosphate binding site with the RhoG C-terminal lipidation site suggests simultaneous binding of RhoG and DOCK5/ELMO1 to the plasma membrane. Structural comparison of the apo and RhoG-bound states revealed that RhoG facilitates a closed-to-open state conformational change of DOCK5/ELMO1. Biochemical and surface plasmon resonance (SPR) assays confirm that RhoG enhances the Rac GEF activity of DOCK5/ELMO1 and increases its binding affinity for Rac1. Further analysis of structural variability underscored the conformational flexibility of the DOCK5/ELMO1/Rac1 complex core, potentially facilitating the proximity of the DOCK5 GEF domain to the plasma membrane. These findings elucidate the structural mechanism underlying the RhoG-induced allosteric activation and membrane binding of the DOCK/ELMO complex. | ||||||||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 422.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 328 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.4 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.5 MB | 表示 | |
XML形式データ | ![]() | 85.5 KB | 表示 | |
CIF形式データ | ![]() | 128.4 KB | 表示 | |
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 | ![]() 38466MC ![]() 8jhkC ![]() 8zj2C ![]() 8zjiC ![]() 8zjjC ![]() 8zjkC ![]() 8zjlC ![]() 8zjmC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 84337.719 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
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#2: タンパク質 | 分子量: 191492.125 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#3: タンパク質 | 分子量: 22362.359 Da / 分子数: 1 / Mutation: Q61L / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
#4: 化合物 | ChemComp-MG / |
#5: 化合物 | ChemComp-GTP / |
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: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: RhoG/DOCK5/ELMO1 complex / タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() |
緩衝液 | pH: 8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 64000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 11976 |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 2483502 | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 4.91 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 181978 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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拘束条件 |
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