+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7uxc | ||||||
---|---|---|---|---|---|---|---|
タイトル | cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion | ||||||
要素 |
| ||||||
キーワード | SIGNALING PROTEIN / mTORC1 / TFEB / Lysosome biogenesis / Autophagy | ||||||
機能・相同性 | 機能・相同性情報 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 / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / RNA polymerase III type 2 promoter sequence-specific DNA binding ...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 / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / antibacterial innate immune response / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / regulation of membrane permeability / heart valve morphogenesis / regulation of TORC1 signaling / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / TORC1 complex / protein localization to lysosome / calcineurin-NFAT signaling cascade / nucleus localization / cellular response to methionine / voluntary musculoskeletal movement / regulation of osteoclast differentiation / regulation of TOR signaling / positive regulation of odontoblast differentiation / TORC1 signaling / positive regulation of keratinocyte migration / endosome organization / fibroblast migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / lysosome localization / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of cell size / ruffle organization / kinase activator activity / protein localization to membrane / protein serine/threonine kinase inhibitor activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / negative regulation of protein localization to nucleus / enzyme-substrate adaptor activity / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / endosomal transport / embryonic placenta development / azurophil granule membrane / negative regulation of macroautophagy / regulation of cell size / small GTPase-mediated signal transduction / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of oligodendrocyte differentiation / Macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / protein kinase activator activity / RHOJ GTPase cycle / oligodendrocyte differentiation / behavioral response to pain / RHOQ GTPase cycle / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / : / tertiary granule membrane / CDC42 GTPase cycle / social behavior / humoral immune response / RHOH GTPase cycle / ficolin-1-rich granule membrane / HSF1-dependent transactivation / neuronal action potential / RHOG GTPase cycle / Transcriptional and post-translational regulation of MITF-M expression and activity / TOR signaling / regulation of receptor recycling / positive regulation of TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / response to amino acid / endomembrane system 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: 3.2 Å | ||||||
データ登録者 | Cui, Z. / Hurley, J. | ||||||
資金援助 | 米国, 1件
| ||||||
引用 | ジャーナル: Nature / 年: 2023 タイトル: Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. 著者: Zhicheng Cui / Gennaro Napolitano / Mariana E G de Araujo / Alessandra Esposito / Jlenia Monfregola / Lukas A Huber / Andrea Ballabio / James H Hurley / 要旨: The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its ...The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its mTORC1 substrate recruitment mechanism, which is strictly dependent on the amino acid-mediated activation of the RagC GTPase activating protein FLCN. TFEB lacks the TOR signalling motif responsible for the recruitment of other mTORC1 substrates. We used cryogenic-electron microscopy to determine the structure of TFEB as presented to mTORC1 for phosphorylation, which we refer to as the 'megacomplex'. Two full Rag-Ragulator complexes present each molecule of TFEB to the mTOR active site. One Rag-Ragulator complex is bound to Raptor in the canonical mode seen previously in the absence of TFEB. A second Rag-Ragulator complex (non-canonical) docks onto the first through a RagC GDP-dependent contact with the second Ragulator complex. The non-canonical Rag dimer binds the first helix of TFEB with a RagC-dependent aspartate clamp in the cleft between the Rag G domains. In cellulo mutation of the clamp drives TFEB constitutively into the nucleus while having no effect on mTORC1 localization. The remainder of the 108-amino acid TFEB docking domain winds around Raptor and then back to RagA. The double use of RagC GDP contacts in both Rag dimers explains the strong dependence of TFEB phosphorylation on FLCN and the RagC GDP state. | ||||||
履歴 |
|
-構造の表示
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 | 7uxc.cif.gz | 2 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb7uxc.ent.gz | 1.6 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7uxc.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
文書・要旨 | 7uxc_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 7uxc_full_validation.pdf.gz | 1.7 MB | 表示 | |
XML形式データ | 7uxc_validation.xml.gz | 160.5 KB | 表示 | |
CIF形式データ | 7uxc_validation.cif.gz | 247.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ux/7uxc ftp://data.pdbj.org/pub/pdb/validation_reports/ux/7uxc | HTTPS FTP |
-関連構造データ
関連構造データ | 26857MC 7ux2C 7uxhC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
---|---|
類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-タンパク質 , 4種, 4分子 ABCR
#1: タンパク質 | 分子量: 289257.969 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: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1 / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: P42345, non-specific serine/threonine protein kinase |
---|---|
#2: タンパク質 | 分子量: 35910.090 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: MLST8, GBL, LST8 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9BVC4 |
#3: タンパク質 | 分子量: 149200.016 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: RPTOR, KIAA1303, RAPTOR / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q8N122 |
#11: タンパク質 | 分子量: 52926.621 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: TFEB, BHLHE35 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P19484 |
-Ras-related GTP-binding protein ... , 2種, 4分子 DKEL
#4: タンパク質 | 分子量: 36600.195 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RRAGA / 発現宿主: Homo sapiens (ヒト) 参照: UniProt: Q7L523, 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 #5: タンパク質 | 分子量: 44298.859 Da / 分子数: 2 / 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: Homo sapiens (ヒト) / 参照: UniProt: Q9HB90 |
---|
-Ragulator complex protein ... , 5種, 10分子 FMGNHOIPJQ
#6: タンパク質 | 分子量: 17762.775 Da / 分子数: 2 / 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q6IAA8 #7: タンパク質 | 分子量: 13517.450 Da / 分子数: 2 / 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q9Y2Q5 #8: タンパク質 | 分子量: 13637.678 Da / 分子数: 2 / 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q9UHA4 #9: タンパク質 | 分子量: 10753.236 Da / 分子数: 2 / 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q0VGL1 #10: タンパク質 | 分子量: 9622.900 Da / 分子数: 2 / 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: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: O43504 |
---|
-非ポリマー , 4種, 7分子
#12: 化合物 | ChemComp-IHP / | ||||
---|---|---|---|---|---|
#13: 化合物 | #14: 化合物 | #15: 化合物 | |
-詳細
研究の焦点であるリガンドがあるか | N |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: The mTORC1-TFEB-Rag-Ragulator complex / タイプ: COMPLEX / Entity ID: #1-#11 / 由来: MULTIPLE SOURCES |
---|---|
緩衝液 | pH: 7.4 |
試料 | 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 |
---|---|
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 FIELD / 最大 デフォーカス(公称値): 2200 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 BIOQUANTUM (6k x 4k) |
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EMソフトウェア |
| ||||||||||||||||||||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 192332 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 96.35 Å2 | ||||||||||||||||||||||||||||||||
拘束条件 |
|