+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4474 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of the mRNA translating and degrading yeast 80S ribosome-Xrn1 nuclease complex | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay / eisosome membrane domain/MCC / sno(s)RNA processing / karyogamy / eukaryotic initiation factor 4G binding / 5'-3' RNA exonuclease activity / tRNA decay / rRNA catabolic process / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / traversing start control point of mitotic cell cycle ...nuclear-transcribed mRNA catabolic process, 5'-3' exonucleolytic nonsense-mediated decay / eisosome membrane domain/MCC / sno(s)RNA processing / karyogamy / eukaryotic initiation factor 4G binding / 5'-3' RNA exonuclease activity / tRNA decay / rRNA catabolic process / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / traversing start control point of mitotic cell cycle / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / 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 / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 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 / negative regulation of macroautophagy / 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 / nuclear-transcribed mRNA catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / positive regulation of transcription initiation by RNA polymerase II / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / positive regulation of transcription elongation by RNA polymerase II / 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 / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / P-body / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / microtubule / 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 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Baker's yeast (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 | Tesina P / Heckel E / Cheng J / Buschauer R / Kater L / Berninghausen O / Becker T / Beckmann R | |||||||||
資金援助 | ドイツ, 2件
| |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2019 タイトル: Structure of the 80S ribosome-Xrn1 nuclease complex. 著者: Petr Tesina / Elisabeth Heckel / Jingdong Cheng / Micheline Fromont-Racine / Robert Buschauer / Lukas Kater / Birgitta Beatrix / Otto Berninghausen / Alain Jacquier / Thomas Becker / Roland Beckmann / 要旨: Messenger RNA (mRNA) homeostasis represents an essential part of gene expression, in which the generation of mRNA by RNA polymerase is counter-balanced by its degradation by nucleases. The conserved ...Messenger RNA (mRNA) homeostasis represents an essential part of gene expression, in which the generation of mRNA by RNA polymerase is counter-balanced by its degradation by nucleases. The conserved 5'-to-3' exoribonuclease Xrn1 has a crucial role in eukaryotic mRNA homeostasis by degrading decapped or cleaved mRNAs post-translationally and, more surprisingly, also co-translationally. Here we report that active Xrn1 can directly and specifically interact with the translation machinery. A cryo-electron microscopy structure of a programmed Saccharomyces cerevisiae 80S ribosome-Xrn1 nuclease complex reveals how the conserved core of Xrn1 enables binding at the mRNA exit site of the ribosome. This interface provides a conduit for channelling of the mRNA from the ribosomal decoding site directly into the active center of the nuclease, thus separating mRNA decoding from degradation by only 17 ± 1 nucleotides. These findings explain how rapid 5'-to-3' mRNA degradation is coupled efficiently to its final round of mRNA translation. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_4474.map.gz | 142.7 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-4474-v30.xml emd-4474.xml | 102.7 KB 102.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4474_fsc.xml | 14.2 KB | 表示 | FSCデータファイル |
画像 | emd_4474.png | 117.7 KB | ||
その他 | emd_4474_additional.map.gz | 142.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4474 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4474 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4474_validation.pdf.gz | 294.7 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_4474_full_validation.pdf.gz | 293.9 KB | 表示 | |
XML形式データ | emd_4474_validation.xml.gz | 13.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4474 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4474 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_4474.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-追加マップ: Focus-refined map using soft mask around Xrn1. Local...
ファイル | emd_4474_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Focus-refined map using soft mask around Xrn1. Local resolution filtered. | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : Yeast 80S ribosome in complex with the Xrn11 exoribonuclease obta...
+超分子 #1: Yeast 80S ribosome in complex with the Xrn11 exoribonuclease obta...
+超分子 #2: ribosome
+超分子 #3: mRNA
+超分子 #4: 5'-3' exoribonuclease Xrn1
+超分子 #5: P-site tRNA
+超分子 #6: E-site tRNA
+分子 #1: 18S ribosomal RNA
+分子 #34: mRNA
+分子 #35: P-site tRNA
+分子 #36: E-site tRNA
+分子 #54: 25S ribosomal RNA
+分子 #55: 5S ribosomal RNA
+分子 #56: 5.8S ribosomal RNA
+分子 #2: 60S ribosomal protein L8-A
+分子 #3: 60S ribosomal protein L23-A
+分子 #4: 60S ribosomal protein L36-A
+分子 #5: 60S ribosomal protein L9-A
+分子 #6: 60S ribosomal protein L24-A
+分子 #7: 60S ribosomal protein L37-A
+分子 #8: 60S ribosomal protein L11-B
+分子 #9: 60S ribosomal protein L25
+分子 #10: 60S ribosomal protein L38
+分子 #11: 60S ribosomal protein L13-A
+分子 #12: 60S ribosomal protein L26-A
+分子 #13: 60S ribosomal protein L39
+分子 #14: 60S ribosomal protein L14-A
+分子 #15: 60S ribosomal protein L27-A
+分子 #16: Ubiquitin-60S ribosomal protein L40
+分子 #17: 60S ribosomal protein L42-A
+分子 #18: 60S ribosomal protein L15-A
+分子 #19: 60S ribosomal protein L28
+分子 #20: 60S ribosomal protein L41-B
+分子 #21: 60S ribosomal protein L43-A
+分子 #22: 60S ribosomal protein L16-A
+分子 #23: 60S ribosomal protein L29
+分子 #24: 60S ribosomal protein L2-A
+分子 #25: 60S ribosomal protein L17-A
+分子 #26: 40S ribosomal protein S21-A
+分子 #27: 40S ribosomal protein S22-A
+分子 #28: 40S ribosomal protein S23-A
+分子 #29: 40S ribosomal protein S24-A
+分子 #30: 40S ribosomal protein S26-B
+分子 #31: 40S ribosomal protein S27-A
+分子 #32: 40S ribosomal protein S30-A
+分子 #33: 5'-3' exoribonuclease 1
+分子 #37: 60S ribosomal protein L30
+分子 #38: 60S ribosomal protein L3
+分子 #39: 60S ribosomal protein L18-A
+分子 #40: 60S ribosomal protein L31-A
+分子 #41: 60S ribosomal protein L10
+分子 #42: 60S ribosomal protein L4-A
+分子 #43: 60S ribosomal protein L19-A
+分子 #44: 60S ribosomal protein L32
+分子 #45: 60S ribosomal protein L20-A
+分子 #46: 60S ribosomal protein L5
+分子 #47: 60S ribosomal protein L21-A
+分子 #48: 60S ribosomal protein L33-A
+分子 #49: 60S ribosomal protein L22-A
+分子 #50: 60S ribosomal protein L6-A
+分子 #51: 60S ribosomal protein L34-A
+分子 #52: 60S ribosomal protein L7-A
+分子 #53: 60S ribosomal protein L35-A
+分子 #57: 40S ribosomal protein S3
+分子 #58: Rps5p
+分子 #59: 40S ribosomal protein S10-A
+分子 #60: 40S ribosomal protein S12
+分子 #61: 40S ribosomal protein S15
+分子 #62: 40S ribosomal protein S16-A
+分子 #63: 40S ribosomal protein S17-A
+分子 #64: 40S ribosomal protein S18-A
+分子 #65: 40S ribosomal protein S20
+分子 #66: 40S ribosomal protein S25-A
+分子 #67: 40S ribosomal protein S28-A
+分子 #68: 40S ribosomal protein S29-A
+分子 #69: Ubiquitin-40S ribosomal protein S31
+分子 #70: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #71: 40S ribosomal protein S0-A
+分子 #72: 40S ribosomal protein S1-A
+分子 #73: 40S ribosomal protein S2
+分子 #74: 40S ribosomal protein S4-A
+分子 #75: 40S ribosomal protein S6-A
+分子 #76: 40S ribosomal protein S7-A
+分子 #77: 40S ribosomal protein S8-A
+分子 #78: 40S ribosomal protein S9-A
+分子 #79: 40S ribosomal protein S11-A
+分子 #80: 40S ribosomal protein S13
+分子 #81: 40S ribosomal protein S14-B
+分子 #82: 40S ribosomal protein S19-A
+分子 #83: ZINC ION
+分子 #84: MAGNESIUM ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 2.5 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 |