+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8rcn | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused region of mTOR and RAPTOR on one protomer copy. | ||||||||||||
要素 |
| ||||||||||||
キーワード | SIGNALING PROTEIN / Target of Rapamycin / mTOR / Cancer-associated mutants | ||||||||||||
機能・相同性 | 機能・相同性情報 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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding / cellular response to leucine starvation ...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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / eukaryotic initiation factor 4E binding / cellular response to leucine starvation / TORC2 complex / TFIIIC-class transcription factor complex binding / regulation of membrane permeability / negative regulation of lysosome organization / heart valve morphogenesis / nucleus localization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / cellular response to methionine / TORC1 signaling / regulation of osteoclast differentiation / voluntary musculoskeletal movement / positive regulation of odontoblast differentiation / positive regulation of keratinocyte migration / cellular response to L-leucine / Amino acids regulate mTORC1 / MTOR signalling / 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 / positive regulation of osteoclast differentiation / protein serine/threonine kinase inhibitor activity / cellular response to osmotic stress / enzyme-substrate adaptor activity / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / regulation of cell size / negative regulation of macroautophagy / positive regulation of oligodendrocyte differentiation / positive regulation of actin filament polymerization / lysosome organization / Macroautophagy / positive regulation of myotube differentiation / protein kinase activator activity / behavioral response to pain / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / : / social behavior / HSF1-dependent transactivation / neuronal action potential / positive regulation of TOR signaling / TOR signaling / response to amino acid / regulation of macroautophagy / cellular response to nutrient levels / positive regulation of translational initiation / positive regulation of G1/S transition of mitotic cell cycle / endomembrane system / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of lamellipodium assembly / phagocytic vesicle / heart morphogenesis / positive regulation of lipid biosynthetic process / positive regulation of epithelial to mesenchymal transition / cardiac muscle contraction / regulation of cellular response to heat / translation repressor activity / negative regulation of translational initiation / cytoskeleton organization / positive regulation of stress fiber assembly / 14-3-3 protein binding / positive regulation of endothelial cell proliferation / phosphorylation / T cell costimulation / translation initiation factor binding / positive regulation of glycolytic process / cellular response to amino acid starvation / negative regulation of autophagy / positive regulation of mitotic cell cycle / cellular response to starvation / response to nutrient levels / response to nutrient / post-embryonic development / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / regulation of signal transduction by p53 class mediator / Regulation of PTEN gene transcription 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: 3.1 Å | ||||||||||||
データ登録者 | Anandapadamanaban, M. / Hay, I.M. / Perisic, O. / Williams, R.L. | ||||||||||||
資金援助 | 英国, European Union, 3件
| ||||||||||||
引用 | ジャーナル: To Be Published タイトル: CryoEM structure of mTORC1 with a paediatric kidney cancer-associated 1455-EWED-1458 duplication in mTOR, Focused region of mTOR and RAPTOR on one protomer copy. 著者: Anandapadamanaban, M. / Hay, I.M. / Perisic, O. / Williams, R.L. | ||||||||||||
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 | 8rcn.cif.gz | 937.4 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb8rcn.ent.gz | 604.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8rcn.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 | 8rcn_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 8rcn_full_validation.pdf.gz | 1.5 MB | 表示 | |
XML形式データ | 8rcn_validation.xml.gz | 67.5 KB | 表示 | |
CIF形式データ | 8rcn_validation.cif.gz | 103.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/rc/8rcn ftp://data.pdbj.org/pub/pdb/validation_reports/rc/8rcn | HTTPS FTP |
-関連構造データ
関連構造データ | 19056MC 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 (文献) |
---|---|
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
#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: 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 | ||
#3: タンパク質 | 分子量: 12592.968 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: EIF4EBP1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q13541 | ||
#4: 化合物 | ChemComp-ANP / | ||
#5: 化合物 | 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 |
---|---|
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: mTORC1 complex is a dimer of a heterotrimeric complex including mTOR, RAPTOR and mLST8. タイプ: COMPLEX 詳細: This paediatric kidney cancer-associated mTORC1 variant consists of mTOR 1455-EWED-1458 duplication, RAPTOR and mLST8 complex and its bound to a substrate 4EBP1. Entity ID: #1-#3 / 由来: RECOMBINANT |
---|---|
分子量 | 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.5 |
試料 | 濃度: 0.6 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 95 % |
-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): 3000 nm / 最小 デフォーカス(公称値): 1200 nm / Cs: 2.7 mm |
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
EMソフトウェア | 名称: EPU / カテゴリ: 画像取得 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | タイプ: NONE | ||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 178379 / アルゴリズム: FOURIER SPACE 詳細: To obtain high-resolution details, the focused refinement of mTOR and RAPTOR region was performed on paediatric kidney cancer-associated mTORC1 variant consists of mTOR 1455-EWED-1458 ...詳細: To obtain high-resolution details, the focused refinement of mTOR and RAPTOR region was performed on paediatric kidney cancer-associated mTORC1 variant consists of mTOR 1455-EWED-1458 duplication, RAPTOR and mLST8 complex and its bound to a substrate 4EBP1. クラス平均像の数: 3 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | B value: 98.5 / プロトコル: FLEXIBLE FIT / 空間: REAL / Target criteria: cross-correlation coefficient 詳細: Initial local fitting was done in Coot and Chimera and then subjected to ROSETTA for model rebuilding. Finally, in Phenix real-space refine was performed for the final model | ||||||||||||||||||||||||
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: 98.45 Å2 | ||||||||||||||||||||||||
拘束条件 |
|