- EMDB-14420: Subtomogram average of 80S ribosomes with additional densities cl... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-14420
タイトル
Subtomogram average of 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired on cryo-FIB-lamellae of S. pombe
マップデータ
Subtomogram average of 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired on cryo-FIB-lamellae of S. pombe
試料
複合体: 80S ribosome with additional densities close to the exit tunnel and the head of the small subunit inside S. pombe cells
ジャーナル: Nat Methods / 年: 2023 タイトル: Convolutional networks for supervised mining of molecular patterns within cellular context. 著者: Irene de Teresa-Trueba / Sara K Goetz / Alexander Mattausch / Frosina Stojanovska / Christian E Zimmerli / Mauricio Toro-Nahuelpan / Dorothy W C Cheng / Fergus Tollervey / Constantin Pape / ...著者: Irene de Teresa-Trueba / Sara K Goetz / Alexander Mattausch / Frosina Stojanovska / Christian E Zimmerli / Mauricio Toro-Nahuelpan / Dorothy W C Cheng / Fergus Tollervey / Constantin Pape / Martin Beck / Alba Diz-Muñoz / Anna Kreshuk / Julia Mahamid / Judith B Zaugg / 要旨: Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning ...Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.
ダウンロード / ファイル: emd_14420.map.gz / 形式: CCP4 / 大きさ: 10.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Subtomogram average of 80S ribosomes with additional densities close to the exit tunnel and the head of the small subunit from tomograms acquired on cryo-FIB-lamellae of S. pombe
ボクセルのサイズ
X=Y=Z: 3.3702 Å
密度
表面レベル
登録者による: 0.37
最小 - 最大
-0.451125 - 1.45089
平均 (標準偏差)
0.03124317 (±0.1403546)
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
140
140
140
Spacing
140
140
140
セル
A=B=C: 471.828 Å α=β=γ: 90.0 °
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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 : 80S ribosome with additional densities close to the exit tunnel a...
全体
名称: 80S ribosome with additional densities close to the exit tunnel and the head of the small subunit inside S. pombe cells
要素
複合体: 80S ribosome with additional densities close to the exit tunnel and the head of the small subunit inside S. pombe cells
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超分子 #1: 80S ribosome with additional densities close to the exit tunnel a...
超分子
名称: 80S ribosome with additional densities close to the exit tunnel and the head of the small subunit inside S. pombe cells タイプ: complex / ID: 1 / 親要素: 0