+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14990 | ||||||||||||
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タイトル | FAP-80S Complex - Rotated state | ||||||||||||
マップデータ | A composite map of Fap1-Yil161w-Fpr1 bound 80S ribosome in rotated state. For individual density, different contour levels are recommended; 80S, tRNAs (3.0); Fap1, Yil161w, Fpr1 (1.5-3.5), mRNA (2.0). | ||||||||||||
試料 |
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キーワード | NRD / Ubiquitination / E3 ligase / Quality Control System / RIBOSOME | ||||||||||||
機能・相同性 | 機能・相同性情報 Calcineurin activates NFAT / regulation of chaperone-mediated protein folding / regulation of homoserine biosynthetic process / macrolide binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity ...Calcineurin activates NFAT / regulation of chaperone-mediated protein folding / regulation of homoserine biosynthetic process / macrolide binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / hexon binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / preribosome, small subunit precursor / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA destabilization / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / regulation of amino acid metabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / Ub-specific processing proteases / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / protein folding chaperone / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / peptidylprolyl isomerase / translational initiation / peptidyl-prolyl cis-trans isomerase activity / protein kinase C binding / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / protein folding / ribosome biogenesis / viral capsid / ribosome binding / chromatin organization / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / cytoplasmic translation / cytosolic large ribosomal subunit / transcription by RNA polymerase II / nucleic acid binding / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / translation / DNA-binding transcription factor activity / negative regulation of gene expression / response to antibiotic 類似検索 - 分子機能 | ||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Saccharomyces cerevisiae W303 (パン酵母) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.4 Å | ||||||||||||
データ登録者 | Ikeuchi K / Buschauer R / Berninghausen O / Becker T / Beckmann R | ||||||||||||
資金援助 | ドイツ, European Union, 3件
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引用 | ジャーナル: Mol Cell / 年: 2022 タイトル: Sensing of individual stalled 80S ribosomes by Fap1 for nonfunctional rRNA turnover. 著者: Sihan Li / Ken Ikeuchi / Misaki Kato / Robert Buschauer / Takato Sugiyama / Shungo Adachi / Hideo Kusano / Tohru Natsume / Otto Berninghausen / Yoshitaka Matsuo / Thomas Becker / Roland ...著者: Sihan Li / Ken Ikeuchi / Misaki Kato / Robert Buschauer / Takato Sugiyama / Shungo Adachi / Hideo Kusano / Tohru Natsume / Otto Berninghausen / Yoshitaka Matsuo / Thomas Becker / Roland Beckmann / Toshifumi Inada / 要旨: Cells can respond to stalled ribosomes by sensing ribosome collisions and employing quality control pathways. How ribosome stalling is resolved without collisions, however, has remained elusive. ...Cells can respond to stalled ribosomes by sensing ribosome collisions and employing quality control pathways. How ribosome stalling is resolved without collisions, however, has remained elusive. Here, focusing on noncolliding stalling exhibited by decoding-defective ribosomes, we identified Fap1 as a stalling sensor triggering 18S nonfunctional rRNA decay via polyubiquitination of uS3. Ribosome profiling revealed an enrichment of Fap1 at the translation initiation site but also an association with elongating individual ribosomes. Cryo-EM structures of Fap1-bound ribosomes elucidated Fap1 probing the mRNA simultaneously at both the entry and exit channels suggesting an mRNA stasis sensing activity, and Fap1 sterically hinders the formation of canonical collided di-ribosomes. Our findings indicate that individual stalled ribosomes are the potential signal for ribosome dysfunction, leading to accelerated turnover of the ribosome itself. | ||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_14990.map.gz | 129.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14990-v30.xml emd-14990.xml | 117.8 KB 117.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_14990.png | 215.7 KB | ||
Filedesc metadata | emd-14990.cif.gz | 20 KB | ||
その他 | emd_14990_additional_1.map.gz emd_14990_additional_2.map.gz emd_14990_additional_3.map.gz emd_14990_additional_4.map.gz emd_14990_additional_5.map.gz emd_14990_additional_6.map.gz | 241.4 MB 34.7 MB 240.4 MB 226.4 MB 242.5 MB 35 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14990 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14990 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14990_validation.pdf.gz | 489.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14990_full_validation.pdf.gz | 489.4 KB | 表示 | |
XML形式データ | emd_14990_validation.xml.gz | 7.9 KB | 表示 | |
CIF形式データ | emd_14990_validation.cif.gz | 9.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14990 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14990 | HTTPS FTP |
-関連構造データ
関連構造データ | 7zw0MC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_14990.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | A composite map of Fap1-Yil161w-Fpr1 bound 80S ribosome in rotated state. For individual density, different contour levels are recommended; 80S, tRNAs (3.0); Fap1, Yil161w, Fpr1 (1.5-3.5), mRNA (2.0). | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.045 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: Multi-body Refinement 1 body 1 - 60S subunit
ファイル | emd_14990_additional_1.map | ||||||||||||
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注釈 | Multi-body Refinement 1 body 1 - 60S subunit | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Multi-body Refinement 2 - Fap1-Arm, Yil161w
ファイル | emd_14990_additional_2.map | ||||||||||||
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注釈 | Multi-body Refinement 2 - Fap1-Arm, Yil161w | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Multi-body Refinement 1 body 2 - 40S body, Fap1-R3H
ファイル | emd_14990_additional_3.map | ||||||||||||
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注釈 | Multi-body Refinement 1 body 2 - 40S body, Fap1-R3H | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Multi-body Refinement 1 body 3 - 40S head, Fap1-mid, Fpr1
ファイル | emd_14990_additional_4.map | ||||||||||||
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注釈 | Multi-body Refinement 1 body 3 - 40S head, Fap1-mid, Fpr1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Consensus Map
ファイル | emd_14990_additional_5.map | ||||||||||||
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注釈 | Consensus Map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Multi-body Refinement 2 - Fap1-RING
ファイル | emd_14990_additional_6.map | ||||||||||||
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注釈 | Multi-body Refinement 2 - Fap1-RING | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Fap1-Yil161w-Fpr1-bound yeast 80S ribosome in rotated state
+超分子 #1: Fap1-Yil161w-Fpr1-bound yeast 80S ribosome in rotated state
+分子 #1: 25S ribosomal RNA (RDN25-1)
+分子 #3: 18S ribosomal RNA (RDN18-1)
+分子 #39: mRNA
+分子 #40: tRNA
+分子 #41: 5S ribosomal RNA (RDN5-1)
+分子 #42: 5.8S ribosomal RNA (RDN58-1)
+分子 #2: 60S ribosomal protein L1-A
+分子 #4: 40S ribosomal protein S0-A
+分子 #5: 40S ribosomal protein S1-A
+分子 #6: RPS15 isoform 1
+分子 #7: 40S ribosomal protein S2
+分子 #8: 40S ribosomal protein S3
+分子 #9: 40S ribosomal protein S4-B
+分子 #10: 40S ribosomal protein S5
+分子 #11: 40S ribosomal protein S6-B
+分子 #12: 40S ribosomal protein S7-A
+分子 #13: 40S ribosomal protein S8-A
+分子 #14: 40S ribosomal protein S9-A
+分子 #15: 40S ribosomal protein S10-A
+分子 #16: 40S ribosomal protein S11-A
+分子 #17: 40S ribosomal protein S12
+分子 #18: 40S ribosomal protein S13
+分子 #19: 40S ribosomal protein S14-A
+分子 #20: 40S ribosomal protein S16-A
+分子 #21: 40S ribosomal protein S17-A
+分子 #22: 40S ribosomal protein S18-A
+分子 #23: 40S ribosomal protein S19-A
+分子 #24: 40S ribosomal protein S20
+分子 #25: 40S ribosomal protein S21-A
+分子 #26: 40S ribosomal protein S22-A
+分子 #27: 40S ribosomal protein S23-A
+分子 #28: 40S ribosomal protein S24-A
+分子 #29: 40S ribosomal protein S25-A
+分子 #30: 40S ribosomal protein S26-A
+分子 #31: 40S ribosomal protein S27-A
+分子 #32: RPS29A isoform 1
+分子 #33: 40S ribosomal protein S30-A
+分子 #34: 40S ribosomal protein S31
+分子 #35: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #36: 40S ribosomal protein S28-A
+分子 #37: Uncharacterized protein YIL161W
+分子 #38: FK506-binding protein 1
+分子 #43: 60S ribosomal protein L2-A
+分子 #44: 60S ribosomal protein L3
+分子 #45: 60S ribosomal protein L4-A
+分子 #46: 60S ribosomal protein L5
+分子 #47: 60S ribosomal protein L6-B
+分子 #48: 60S ribosomal protein L7-A
+分子 #49: 60S ribosomal protein L8-A
+分子 #50: 60S ribosomal protein L9-A
+分子 #51: 60S ribosomal protein L10
+分子 #52: 60S ribosomal protein L11-A
+分子 #53: 60S ribosomal protein L13-A
+分子 #54: 60S ribosomal protein L14-A
+分子 #55: 60S ribosomal protein L15-A
+分子 #56: 60S ribosomal protein L16-A
+分子 #57: 60S ribosomal protein L17-A
+分子 #58: 60S ribosomal protein L18-A
+分子 #59: 60S ribosomal protein L19-A
+分子 #60: 60S ribosomal protein L20-A
+分子 #61: 60S ribosomal protein L21-A
+分子 #62: 60S ribosomal protein L22-A
+分子 #63: 60S ribosomal protein L23-A
+分子 #64: 60S ribosomal protein L24-A
+分子 #65: 60S ribosomal protein L25
+分子 #66: 60S ribosomal protein L26-A
+分子 #67: 60S ribosomal protein L27-A
+分子 #68: 60S ribosomal protein L28
+分子 #69: 60S ribosomal protein L29
+分子 #70: 60S ribosomal protein L30
+分子 #71: 60S ribosomal protein L31-A
+分子 #72: 60S ribosomal protein L32
+分子 #73: 60S ribosomal protein L33-A
+分子 #74: 60S ribosomal protein L34-A
+分子 #75: 60S ribosomal protein L35-A
+分子 #76: 60S ribosomal protein L36-A
+分子 #77: 60S ribosomal protein L37-A
+分子 #78: 60S ribosomal protein L38
+分子 #79: 60S ribosomal protein L39
+分子 #80: 60S ribosomal protein L40-A
+分子 #81: 60S ribosomal protein L41-A
+分子 #82: 60S ribosomal protein L42-A
+分子 #83: 60S ribosomal protein L43-A
+分子 #84: FAP1 isoform 1
+分子 #85: MAGNESIUM ION
+分子 #86: SPERMIDINE
+分子 #87: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 43.4 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 114964 |
初期 角度割当 | タイプ: NOT APPLICABLE |
最終 角度割当 | タイプ: NOT APPLICABLE |