- EMDB-0232: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-0232
タイトル
Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3
マップデータ
map of the T. brucei mitoribosome small subunit body in complex with mt-IF3
試料
複合体: body of the T. brucei mitoribosome small subunit in complex with mt-IF-3
タンパク質・ペプチド: x 40種
RNA: x 1種
リガンド: x 4種
機能・相同性
機能・相同性情報
modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-ヒドロキシイソブチリルCoAヒドロラーゼ / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / valine catabolic process / キネトプラスト / クオラムセンシング / enoyl-CoA hydratase activity ...modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-ヒドロキシイソブチリルCoAヒドロラーゼ / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / valine catabolic process / キネトプラスト / クオラムセンシング / enoyl-CoA hydratase activity / regulation of protein kinase A signaling / mRNA stabilization / ciliary plasm / mitochondrial small ribosomal subunit / fatty acid beta-oxidation / スーパーオキシドディスムターゼ / protein kinase A regulatory subunit binding / superoxide dismutase activity / cytosolic small ribosomal subunit / hydrolase activity / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / ミトコンドリア / RNA binding / metal ion binding / 細胞質基質 / 細胞質 類似検索 - 分子機能
Nucleoid-associated protein YbaB-like domain superfamily / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / : / Probable Zinc-ribbon domain / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 ...Nucleoid-associated protein YbaB-like domain superfamily / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / Probable Zinc-ribbon domain / : / Probable Zinc-ribbon domain / Enoyl-CoA hydratase/isomerase domain / Enoyl-CoA hydratase/isomerase, HIBYL-CoA-H type / Enoyl-CoA hydratase/isomerase / Protein Fyv4 / IGR protein motif / IGR / Cyclic phosphodiesterase / Manganese/iron superoxide dismutase, C-terminal / Manganese/iron superoxide dismutase, C-terminal domain superfamily / Iron/manganese superoxide dismutases, C-terminal domain / Manganese/iron superoxide dismutase, N-terminal domain superfamily / ClpP/crotonase-like domain superfamily / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 superfamily / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ubiquitin family / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / Ribosomal protein S9 / Ribosomal protein S9/S16 / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ubiquitin domain profile. / ユビキチン様タンパク質 / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold 類似検索 - ドメイン・相同性
A-kinase anchor protein 7-like phosphoesterase domain-containing protein / Uncharacterized protein / 3-ヒドロキシイソブチリルCoAヒドロラーゼ / Uncharacterized protein / Uncharacterized protein / Probable Zinc-ribbon domain-containing protein / 30S ribosomal protein S8, putative / Small ribosomal subunit protein mS41 / Uncharacterized protein / Mitochondrial ribosomal protein S18 ...A-kinase anchor protein 7-like phosphoesterase domain-containing protein / Uncharacterized protein / 3-ヒドロキシイソブチリルCoAヒドロラーゼ / Uncharacterized protein / Uncharacterized protein / Probable Zinc-ribbon domain-containing protein / 30S ribosomal protein S8, putative / Small ribosomal subunit protein mS41 / Uncharacterized protein / Mitochondrial ribosomal protein S18 / Small ribosomal subunit protein uS5 C-terminal domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Trans-sialidase / Uncharacterized protein / 30S Ribosomal protein S17, putative / Uncharacterized protein / Opioid growth factor receptor (OGFr) conserved domain-containing protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ribosomal protein S23 mitochondrial conserved domain-containing protein / Uncharacterized protein / Ribosomal protein S9 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Ubiquitin-like domain-containing protein / Manganese/iron superoxide dismutase C-terminal domain-containing protein / Superoxide dismutase, putative / Uncharacterized protein / Uncharacterized protein 類似検索 - 構成要素
ジャーナル: Science / 年: 2018 タイトル: Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. 著者: David J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban / 要旨: Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , ...Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements.
フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 平均電子線量: 40.0 e/Å2
実験機器
モデル: Titan Krios / 画像提供: FEI Company
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画像解析
CTF補正
ソフトウェア - 名称: CTFFIND
初期モデル
モデルのタイプ: OTHER / 詳細: initial model from 2D class averages in EMAN
初期 角度割当
タイプ: OTHER
最終 3次元分類
ソフトウェア - 名称: RELION
最終 角度割当
タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION
最終 再構成
アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 3.27 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 31911
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原子モデル構築 1
詳細
We used Coot and O for initial model building and refined the structure using Phenix
精密化
プロトコル: AB INITIO MODEL / 温度因子: 41.4
得られたモデル
PDB-6hiy: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3