- EMDB-2990: Structure of Target Of Rapapmycin Complex 2 (TORC2) from Saccharo... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-2990
タイトル
Structure of Target Of Rapapmycin Complex 2 (TORC2) from Saccharomyces cerevisiae
マップデータ
Reconstruction of yeast TORC2 - filtered at 26 Angstroms resolution (FSC 0.143 criterion after gold standard refinement). Contour level provided by author - The map was generated from negative stain data, and we determined the correct contour level to display the map to be 2.9 in Pymol.
試料
試料: Yeast Target of Rapamycin Complex 2
タンパク質・ペプチド: Yeast TORC2
キーワード
TOR kinase complex / TORC2 / cell growth / rapamycin
ジャーナル: Mol Cell / 年: 2015 タイトル: Molecular Basis of the Rapamycin Insensitivity of Target Of Rapamycin Complex 2. 著者: Christl Gaubitz / Taiana M Oliveira / Manoel Prouteau / Alexander Leitner / Manikandan Karuppasamy / Georgia Konstantinidou / Delphine Rispal / Sandra Eltschinger / Graham C Robinson / ...著者: Christl Gaubitz / Taiana M Oliveira / Manoel Prouteau / Alexander Leitner / Manikandan Karuppasamy / Georgia Konstantinidou / Delphine Rispal / Sandra Eltschinger / Graham C Robinson / Stéphane Thore / Ruedi Aebersold / Christiane Schaffitzel / Robbie Loewith / 要旨: Target of Rapamycin (TOR) plays central roles in the regulation of eukaryote growth as the hub of two essential multiprotein complexes: TORC1, which is rapamycin-sensitive, and the lesser ...Target of Rapamycin (TOR) plays central roles in the regulation of eukaryote growth as the hub of two essential multiprotein complexes: TORC1, which is rapamycin-sensitive, and the lesser characterized TORC2, which is not. TORC2 is a key regulator of lipid biosynthesis and Akt-mediated survival signaling. In spite of its importance, its structure and the molecular basis of its rapamycin insensitivity are unknown. Using crosslinking-mass spectrometry and electron microscopy, we determined the architecture of TORC2. TORC2 displays a rhomboid shape with pseudo-2-fold symmetry and a prominent central cavity. Our data indicate that the C-terminal part of Avo3, a subunit unique to TORC2, is close to the FKBP12-rapamycin-binding domain of Tor2. Removal of this sequence generated a FKBP12-rapamycin-sensitive TORC2 variant, which provides a powerful tool for deciphering TORC2 function in vivo. Using this variant, we demonstrate a role for TORC2 in G2/M cell-cycle progression.
ダウンロード / ファイル: emd_2990.map.gz / 形式: CCP4 / 大きさ: 3.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Reconstruction of yeast TORC2 - filtered at 26 Angstroms resolution (FSC 0.143 criterion after gold standard refinement). Contour level provided by author - The map was generated from negative stain data, and we determined the correct contour level to display the map to be 2.9 in Pymol.
ボクセルのサイズ
X=Y=Z: 4.5 Å
密度
表面レベル
登録者による: 0.029 / ムービー #1: 0.029
最小 - 最大
-0.0818112 - 0.11751353
平均 (標準偏差)
0.00042925 (±0.00938699)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
100
100
100
Spacing
100
100
100
セル
A=B=C: 450.0 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
4.5
4.5
4.5
M x/y/z
100
100
100
origin x/y/z
0.000
0.000
0.000
length x/y/z
450.000
450.000
450.000
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
100
100
100
D min/max/mean
-0.082
0.118
0.000
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添付データ
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試料の構成要素
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全体 : Yeast Target of Rapamycin Complex 2
全体
名称: Yeast Target of Rapamycin Complex 2
要素
試料: Yeast Target of Rapamycin Complex 2
タンパク質・ペプチド: Yeast TORC2
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超分子 #1000: Yeast Target of Rapamycin Complex 2
超分子
名称: Yeast Target of Rapamycin Complex 2 / タイプ: sample / ID: 1000 / 詳細: TORC2 complex, which consists of six subunits / 集合状態: dimer / Number unique components: 1
分子量
実験値: 1.4 MDa / 理論値: 1.4 MDa / 手法: Size exclusion
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分子 #1: Yeast TORC2
分子
名称: Yeast TORC2 / タイプ: protein_or_peptide / ID: 1 詳細: TORC2 is composed of two copies of: Tor2 kinase, Lst8, Avo1, Avo2, Avo3, Bit61/2 コピー数: 1 / 集合状態: 2 / 組換発現: No
照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 倍率(公称値): 26000
試料ステージ
試料ホルダーモデル: SIDE ENTRY, EUCENTRIC / Tilt angle max: 45
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画像解析
詳細
A total of 8,762 RCT pairs were picked manually with tiltpicker (Voss et al, 2009). The additional untilted particles were picked with e2boxer.py (Ludtke, 2010). The 3D reconstruction was calculated with the Xmipp ML tomo and refined with Xmipp MLF 3D (Scheres et al., 2008)
CTF補正
詳細: each micrograph
最終 再構成
想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 26.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Xmipp, Relion / 使用した粒子像数: 24979