+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6ulg | ||||||||||||||||||||||||
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タイトル | Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex | ||||||||||||||||||||||||
要素 |
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キーワード | SIGNALING PROTEIN / FLCN-FNIP2 / Rag GTPases / Ragulator | ||||||||||||||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex ...negative regulation of cell proliferation involved in kidney development / negative regulation of mitochondrial DNA metabolic process / negative regulation of muscle tissue development / negative regulation of post-translational protein modification / cell proliferation involved in kidney development / : / 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 / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / negative regulation of cellular respiration / FNIP-folliculin RagC/D GAP / Ragulator complex / negative regulation of brown fat cell differentiation / regulation of Ras protein signal transduction / protein localization to cell junction / : / regulation of TORC1 signaling / negative regulation of lysosome organization / negative regulation of ATP biosynthetic process / regulation of pro-B cell differentiation / protein localization to lysosome / TORC1 signaling / regulation of TOR signaling / endosome organization / ATPase inhibitor activity / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of TOR signaling / kinase activator activity / protein localization to membrane / enzyme-substrate adaptor activity / enzyme inhibitor activity / negative regulation of glycolytic process / cell-cell junction assembly / negative regulation of protein localization to nucleus / negative regulation of cold-induced thermogenesis / negative regulation of Rho protein signal transduction / azurophil granule membrane / endosomal transport / オートファジー / regulation of cell size / lysosome organization / small GTPase-mediated signal transduction / RHOJ GTPase cycle / MTOR / RHOQ GTPase cycle / positive regulation of transforming growth factor beta receptor signaling pathway / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / RHOH GTPase cycle / CDC42 GTPase cycle / 造血 / ficolin-1-rich granule membrane / centriolar satellite / RHOG GTPase cycle / positive regulation of cell adhesion / positive regulation of TOR signaling / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of receptor recycling / RAC2 GTPase cycle / RAC3 GTPase cycle / response to amino acid / specific granule membrane / positive regulation of autophagy / energy homeostasis / protein-membrane adaptor activity / positive regulation of intrinsic apoptotic signaling pathway / ERK1 and ERK2 cascade / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / cellular response to amino acid starvation / RAC1 GTPase cycle / cellular response to starvation / GTPase activator activity / viral genome replication / intrinsic apoptotic signaling pathway / negative regulation of autophagy / guanyl-nucleotide exchange factor activity / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / RNA splicing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of cytokinesis / Regulation of PTEN gene transcription / cholesterol homeostasis / epithelial cell proliferation / regulation of cell growth / positive regulation of interleukin-8 production / positive regulation of protein-containing complex assembly / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / phosphoprotein binding / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 類似検索 - 分子機能 | ||||||||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||||||||
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: 3.31 Å | ||||||||||||||||||||||||
データ登録者 | Shen, K. / Rogala, K.B. / Yu, Z.H. / Sabatini, D.M. | ||||||||||||||||||||||||
資金援助 | 米国, 7件
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引用 | ジャーナル: Cell / 年: 2019 タイトル: Cryo-EM Structure of the Human FLCN-FNIP2-Rag-Ragulator Complex. 著者: Kuang Shen / Kacper B Rogala / Hui-Ting Chou / Rick K Huang / Zhiheng Yu / David M Sabatini / 要旨: mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN- ...mTORC1 controls anabolic and catabolic processes in response to nutrients through the Rag GTPase heterodimer, which is regulated by multiple upstream protein complexes. One such regulator, FLCN-FNIP2, is a GTPase activating protein (GAP) for RagC/D, but despite its important role, how it activates the Rag GTPase heterodimer remains unknown. We used cryo-EM to determine the structure of FLCN-FNIP2 in a complex with the Rag GTPases and Ragulator. FLCN-FNIP2 adopts an extended conformation with two pairs of heterodimerized domains. The Longin domains heterodimerize and contact both nucleotide binding domains of the Rag heterodimer, while the DENN domains interact at the distal end of the structure. Biochemical analyses reveal a conserved arginine on FLCN as the catalytic arginine finger and lead us to interpret our structure as an on-pathway intermediate. These data reveal features of a GAP-GTPase interaction and the structure of a critical component of the nutrient-sensing mTORC1 pathway. | ||||||||||||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6ulg.cif.gz | 389.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6ulg.ent.gz | 309.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6ulg.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ul/6ulg ftp://data.pdbj.org/pub/pdb/validation_reports/ul/6ulg | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 2種, 2分子 LN
#1: タンパク質 | 分子量: 64551.191 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FLCN, BHD / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8NFG4 |
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#9: タンパク質 | 分子量: 122260.195 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FNIP2, FNIPL, KIAA1450, MAPO1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9P278 |
-Ragulator complex protein ... , 5種, 5分子 ABCDE
#2: 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) Homo sapiens (ヒト) / 遺伝子: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9UHA4 |
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#3: タンパク質 | 分子量: 13517.450 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LAMTOR2, MAPBPIP, ROBLD3, HSPC003 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9Y2Q5 |
#4: タンパク質 | 分子量: 9622.900 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LAMTOR5, HBXIP, XIP / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O43504 |
#5: 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) Homo sapiens (ヒト) / 遺伝子: LAMTOR4, C7orf59 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q0VGL1 |
#6: タンパク質 | 分子量: 17762.775 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LAMTOR1, C11orf59, PDRO, PP7157 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6IAA8 |
-Ras-related GTP-binding protein ... , 2種, 2分子 FG
#7: タンパク質 | 分子量: 36628.168 Da / 分子数: 1 / Mutation: T21N / 由来タイプ: 組換発現 / 詳細: RagA containing a T21N mutation / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RRAGA / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q7L523 |
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#8: タンパク質 | 分子量: 44271.832 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RRAGC / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9HB90 |
-非ポリマー , 3種, 3分子
#10: 化合物 | ChemComp-GDP / |
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#11: 化合物 | ChemComp-GNP / |
#12: 化合物 | ChemComp-MG / |
-詳細
研究の焦点であるリガンドがあるか | N |
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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 |
-試料調製
構成要素 | 名称: Nonameric complex of FLCN-FNIP2 with its substrate Rag GTPases and the scaffolding protein complex Ragulator タイプ: COMPLEX / Entity ID: #1-#9 / 由来: RECOMBINANT |
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分子量 | 値: 0.38 MDa / 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 7.4 |
試料 | 濃度: 8 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
撮影 | 電子線照射量: 59.2 e/Å2 フィルム・検出器のモデル: GATAN K2 BASE (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.16_3549: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.31 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 126984 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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