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基本情報
登録情報 | データベース: PDB / ID: 6nzd | ||||||
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タイトル | Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator) | ||||||
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![]() | signaling protein/inhibitor / Lysosome / mTORC1 regulation / Amino acid sensing / GTPase / SIGNALING PROTEIN / signaling protein-inhibitor complex | ||||||
機能・相同性 | ![]() negative regulation of cell proliferation involved in kidney development / cell proliferation involved in kidney development / negative regulation of post-translational protein modification / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / FNIP-folliculin RagC/D GAP / Ragulator complex ...negative regulation of cell proliferation involved in kidney development / cell proliferation involved in kidney development / negative regulation of post-translational protein modification / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / FNIP-folliculin RagC/D GAP / Ragulator complex / regulation of Ras protein signal transduction / negative regulation of brown fat cell differentiation / protein localization to cell junction / regulation of TORC1 signaling / regulation of pro-B cell differentiation / negative regulation of lysosome organization / protein localization to lysosome / regulation of TOR signaling / Amino acids regulate mTORC1 / fibroblast migration / MTOR signalling / lysosome localization / endosome organization / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / ATPase inhibitor activity / cell-cell junction assembly / protein localization to membrane / kinase activator activity / negative regulation of glycolytic process / negative regulation of TOR signaling / negative regulation of cold-induced thermogenesis / endosomal transport / azurophil granule membrane / lysosome organization / small GTPase-mediated signal transduction / regulation of cell size / Macroautophagy / negative regulation of Rho protein signal transduction / positive regulation of transforming growth factor beta receptor signaling pathway / RHOJ GTPase cycle / RHOQ GTPase cycle / hemopoiesis / TOR signaling / regulation of protein phosphorylation / mTORC1-mediated signalling / tertiary granule membrane / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOH GTPase cycle / enzyme inhibitor activity / RHOG GTPase cycle / regulation of receptor recycling / positive regulation of TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / enzyme-substrate adaptor activity / positive regulation of peptidyl-serine phosphorylation / response to amino acid / cellular response to nutrient levels / specific granule membrane / energy homeostasis / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / tumor necrosis factor-mediated signaling pathway / ERK1 and ERK2 cascade / RAC1 GTPase cycle / positive regulation of autophagy / positive regulation of TORC1 signaling / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of autophagy / intrinsic apoptotic signaling pathway / GTPase activator activity / cellular response to amino acid starvation / transforming growth factor beta receptor signaling pathway / RNA splicing / viral genome replication / cholesterol homeostasis / guanyl-nucleotide exchange factor activity / cellular response to starvation / epithelial cell proliferation / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cell growth / positive regulation of protein-containing complex assembly / MAP2K and MAPK activation / negative regulation of ERK1 and ERK2 cascade / centriolar satellite / response to virus / positive regulation of protein localization to nucleus / intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of epithelial cell proliferation / mitotic spindle / GDP binding / late endosome membrane / late endosome 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: 3.6 Å | ||||||
![]() | Fromm, S.A. / Young, L.N. / Hurley, J.H. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural mechanism of a Rag GTPase activation checkpoint by the lysosomal folliculin complex. 著者: Rosalie E Lawrence / Simon A Fromm / Yangxue Fu / Adam L Yokom / Do Jin Kim / Ashley M Thelen / Lindsey N Young / Chun-Yan Lim / Avi J Samelson / James H Hurley / Roberto Zoncu / ![]() 要旨: The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) ...The tumor suppressor folliculin (FLCN) enables nutrient-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) protein kinase via its guanosine triphosphatase (GTPase) activating protein (GAP) activity toward the GTPase RagC. Concomitant with mTORC1 inactivation by starvation, FLCN relocalizes from the cytosol to lysosomes. To determine the lysosomal function of FLCN, we reconstituted the human lysosomal FLCN complex (LFC) containing FLCN, its partner FLCN-interacting protein 2 (FNIP2), and the RagA:RagC GTPases as they exist in the starved state with their lysosomal anchor Ragulator complex and determined its cryo-electron microscopy structure to 3.6 angstroms. The RagC-GAP activity of FLCN was inhibited within the LFC, owing to displacement of a catalytically required arginine in FLCN from the RagC nucleotide. Disassembly of the LFC and release of the RagC-GAP activity of FLCN enabled mTORC1-dependent regulation of the master regulator of lysosomal biogenesis, transcription factor E3, implicating the LFC as a checkpoint in mTORC1 signaling. | ||||||
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構造の表示
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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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ダウンロード
PDBx/mmCIF形式 | ![]() | 357.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 259.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 928.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 952 KB | 表示 | |
XML形式データ | ![]() | 60.4 KB | 表示 | |
CIF形式データ | ![]() | 91.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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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
-Ragulator complex protein ... , 4種, 4分子 ABCD
#1: タンパク質 | 分子量: 18325.350 Da / 分子数: 1 / 変異: G2A / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q6IAA8 |
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#2: タンパク質 | 分子量: 13645.579 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9Y2Q5 |
#3: タンパク質 | 分子量: 13637.678 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9UHA4 |
#4: タンパク質 | 分子量: 10753.236 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q0VGL1 |
-タンパク質 , 3種, 3分子 EHI
#5: タンパク質 | 分子量: 18178.520 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: A0A0C4DGV4, UniProt: O43504*PLUS |
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#8: タンパク質 | 分子量: 69143.070 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
#9: タンパク質 | 分子量: 122475.414 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() |
-Ras-related GTP-binding protein ... , 2種, 2分子 FG
#6: タンパク質 | 分子量: 36615.168 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q7L523 |
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#7: タンパク質 | 分子量: 44758.336 Da / 分子数: 1 / 変異: D181N / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q9HB90 |
-非ポリマー , 2種, 2分子 


#10: 化合物 | ChemComp-GDP / |
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#11: 化合物 | ChemComp-L8S / |
-詳細
Has protein modification | Y |
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-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: FLCN-FNIP2-RagA-RagC-Ragulator Complex / タイプ: COMPLEX / 詳細: RagA bound to GDP; RagC bound to XTPgammaS / Entity ID: #1-#9 / 由来: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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分子量 | 値: 0.34 MDa / 実験値: NO | ||||||||||||||||||||||||||||||
由来(天然) | 生物種: ![]() | ||||||||||||||||||||||||||||||
由来(組換発現) | 生物種: ![]() ![]() | ||||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.5 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||
試料支持 | 詳細: 15 W / 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: C-flat-2/1 | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 90 % / 凍結前の試料温度: 277 K / 詳細: Whatman 597 |
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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 / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 11 sec. / 電子線照射量: 65.6 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 撮影したグリッド数: 1 / 実像数: 2703 |
電子光学装置 | エネルギーフィルタースリット幅: 20 eV |
画像スキャン | 動画フレーム数/画像: 44 |
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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: 982343 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 163376 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 空間: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Source name: PDB / タイプ: experimental model
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精密化 | 最高解像度: 3.6 Å |