+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10537 | |||||||||
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タイトル | Yeast 80S ribosome in complex with eIF5A and decoding A-site and P-site tRNAs. | |||||||||
マップデータ | Cryo-EM density of the yeast 80S ribosome in complex with eIF5A and A-site and P-site tRNAs. Filtered according to local resolution. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / 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 / positive regulation of translational fidelity ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / 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 / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / translational elongation / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G-protein alpha-subunit binding / positive regulation of protein kinase activity / protein-RNA complex assembly / positive regulation of translational initiation / regulation of translational fidelity / ribosomal small subunit export from nucleus / translation regulator activity / translation elongation factor activity / ribosomal subunit export from nucleus / 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 / translation initiation factor activity / cellular response to amino acid starvation / ribosome assembly / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / macroautophagy / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / maintenance of translational fidelity / ribosomal large subunit assembly / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (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: 3.1 Å | |||||||||
データ登録者 | Buschauer R / Cheng J / Berninghausen O / Tesina P / Becker T / Beckmann R | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Science / 年: 2020 タイトル: The Ccr4-Not complex monitors the translating ribosome for codon optimality. 著者: Robert Buschauer / Yoshitaka Matsuo / Takato Sugiyama / Ying-Hsin Chen / Najwa Alhusaini / Thomas Sweet / Ken Ikeuchi / Jingdong Cheng / Yasuko Matsuki / Risa Nobuta / Andrea Gilmozzi / Otto ...著者: Robert Buschauer / Yoshitaka Matsuo / Takato Sugiyama / Ying-Hsin Chen / Najwa Alhusaini / Thomas Sweet / Ken Ikeuchi / Jingdong Cheng / Yasuko Matsuki / Risa Nobuta / Andrea Gilmozzi / Otto Berninghausen / Petr Tesina / Thomas Becker / Jeff Coller / Toshifumi Inada / Roland Beckmann / 要旨: Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA ...Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo-electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in This interaction occurred when the ribosome lacked accommodated A-site transfer RNA, indicative of low codon optimality. Loss of the interaction resulted in the inability of the mRNA degradation machinery to sense codon optimality. Our findings elucidate a physical link between the Ccr4-Not complex and the ribosome and provide mechanistic insight into the coupling of decoding efficiency with mRNA stability. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_10537.map.gz | 235.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10537-v30.xml emd-10537.xml | 89.2 KB 89.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10537_fsc.xml | 16.9 KB | 表示 | FSCデータファイル |
画像 | emd_10537.png | 89.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10537 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10537 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10537_validation.pdf.gz | 280.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10537_full_validation.pdf.gz | 279.4 KB | 表示 | |
XML形式データ | emd_10537_validation.xml.gz | 15.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10537 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10537 | HTTPS FTP |
-関連構造データ
-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_10537.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 | Cryo-EM density of the yeast 80S ribosome in complex with eIF5A and A-site and P-site tRNAs. Filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : Yeast 80S ribosome in complex with eIF5A programed by A-site and ...
+超分子 #1: Yeast 80S ribosome in complex with eIF5A programed by A-site and ...
+分子 #1: 18S rRNA
+分子 #2: mRNA
+分子 #24: P-site tRNA
+分子 #37: A-site tRNA
+分子 #38: 25S rRNA
+分子 #39: 5S rRNA
+分子 #40: 5.8S rRNA
+分子 #3: 40S ribosomal protein S0-A
+分子 #4: 40S ribosomal protein S1-A
+分子 #5: 40S ribosomal protein S15
+分子 #6: 40S ribosomal protein S2
+分子 #7: 40S ribosomal protein S3
+分子 #8: 40S ribosomal protein S4-A
+分子 #9: Rps5p
+分子 #10: 40S ribosomal protein S6-A
+分子 #11: 40S ribosomal protein S7-A
+分子 #12: 40S ribosomal protein S8
+分子 #13: 40S ribosomal protein S9-A
+分子 #14: 40S ribosomal protein S10-A
+分子 #15: 40S ribosomal protein S11-A
+分子 #16: 40S ribosomal protein S12
+分子 #17: 40S ribosomal protein S13
+分子 #18: 40S ribosomal protein S14-B
+分子 #19: 40S ribosomal protein S16-A
+分子 #20: 40S ribosomal protein S17-B
+分子 #21: 40S ribosomal protein S18-A
+分子 #22: 40S ribosomal protein S19-A
+分子 #23: 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-B
+分子 #31: 40S ribosomal protein S27-A
+分子 #32: 40S ribosomal protein S29-A
+分子 #33: 40S ribosomal protein S30-A
+分子 #34: Ubiquitin-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 #41: 60S ribosomal protein L2-A
+分子 #42: 60S ribosomal protein L3
+分子 #43: 60S ribosomal protein L4-A
+分子 #44: 60S ribosomal protein L5
+分子 #45: 60S ribosomal protein L6-B
+分子 #46: 60S ribosomal protein L7-A
+分子 #47: 60S ribosomal protein L8-A
+分子 #48: 60S ribosomal protein L9-A
+分子 #49: 60S ribosomal protein L10
+分子 #50: 60S ribosomal protein L11-B
+分子 #51: 60S ribosomal protein L13-A
+分子 #52: 60S ribosomal protein L14-A
+分子 #53: 60S ribosomal protein L15-A
+分子 #54: 60S ribosomal protein L16-A
+分子 #55: 60S ribosomal protein L17-A
+分子 #56: 60S ribosomal protein L18-A
+分子 #57: 60S ribosomal protein L19-A
+分子 #58: 60S ribosomal protein L20-A
+分子 #59: 60S ribosomal protein L21-A
+分子 #60: 60S ribosomal protein L22-A
+分子 #61: 60S ribosomal protein L23-A
+分子 #62: 60S ribosomal protein L24-A
+分子 #63: 60S ribosomal protein L25
+分子 #64: 60S ribosomal protein L26-A
+分子 #65: 60S ribosomal protein L27-A
+分子 #66: 60S ribosomal protein L28
+分子 #67: 60S ribosomal protein L29
+分子 #68: 60S ribosomal protein L30
+分子 #69: 60S ribosomal protein L31-A
+分子 #70: 60S ribosomal protein L32
+分子 #71: 60S ribosomal protein L33-A
+分子 #72: 60S ribosomal protein L34-A
+分子 #73: 60S ribosomal protein L35-A
+分子 #74: 60S ribosomal protein L36-A
+分子 #75: 60S ribosomal protein L37-A
+分子 #76: 60S ribosomal protein L38
+分子 #77: 60S ribosomal protein L39
+分子 #78: Ubiquitin-60S ribosomal protein L40
+分子 #79: 60S ribosomal protein L41-A
+分子 #80: 60S ribosomal protein L42-A
+分子 #81: 60S ribosomal protein L43-A
+分子 #82: Eukaryotic translation initiation factor 5A-1
+分子 #83: 60S ribosomal protein L1
+分子 #84: ZINC ION
+分子 #85: SPERMIDINE
+分子 #86: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-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: 7.4 |
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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: FEI FALCON III (4k x 4k) 平均電子線量: 28.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |