+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16127 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Yeast 80S, ES7s delta, eIF5A, Stm1 containing | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
キーワード | eIF5A / Stm1 / Rpl41A / delta ES7s / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of translational termination / ribosomal subunit / positive regulation of translational elongation / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / pre-mRNA 5'-splice site binding ...positive regulation of translational termination / ribosomal subunit / positive regulation of translational elongation / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / 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 / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / regulation of translational fidelity / protein-RNA complex assembly / translation regulator activity / translation elongation factor activity / ribosomal subunit export from nucleus / 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) / cellular response to amino acid starvation / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-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 / 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 / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / 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 / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 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: 2.4 Å | |||||||||
データ登録者 | Dimitrova-Paternoga L / Paternoga H / Wilson DN | |||||||||
資金援助 | ドイツ, スイス, 2件
| |||||||||
引用 | ジャーナル: Nucleic Acids Res / 年: 2024 タイトル: Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. 著者: Robert Rauscher / Cristian Eggers / Lyudmila Dimitrova-Paternoga / Vaishnavi Shankar / Alessia Rosina / Marina Cristodero / Helge Paternoga / Daniel N Wilson / Sebastian A Leidel / Norbert Polacek / 要旨: Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms ...Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center. | |||||||||
履歴 |
|
-構造の表示
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_16127.map.gz | 337.5 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-16127-v30.xml emd-16127.xml | 100.2 KB 100.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_16127.png | 139 KB | ||
Filedesc metadata | emd-16127.cif.gz | 19.2 KB | ||
その他 | emd_16127_half_map_1.map.gz emd_16127_half_map_2.map.gz | 338.7 MB 338.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16127 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16127 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16127_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_16127_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_16127_validation.xml.gz | 18 KB | 表示 | |
CIF形式データ | emd_16127_validation.cif.gz | 21.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16127 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16127 | HTTPS FTP |
-関連構造データ
関連構造データ | 8bn3MC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
---|---|
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 |
---|---|
「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_16127.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 0.783 Å | ||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-ハーフマップ: #2
ファイル | emd_16127_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_16127_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : Dormant yeast 80S ribosome
+超分子 #1: Dormant yeast 80S ribosome
+分子 #1: 60S ribosomal protein L1-A
+分子 #2: Rps5p
+分子 #3: Small ribosomal subunit protein eS10A
+分子 #4: 40S ribosomal protein S14-B
+分子 #5: RPS15 isoform 1
+分子 #6: 40S ribosomal protein S18-A
+分子 #7: RPS20 isoform 1
+分子 #8: 40S ribosomal protein S25
+分子 #9: RPS28A isoform 1
+分子 #10: 60S ribosomal protein L41-A
+分子 #15: Small ribosomal subunit protein uS2A
+分子 #16: Small ribosomal subunit protein eS1
+分子 #17: RPS2 isoform 1
+分子 #18: 40S ribosomal protein S3
+分子 #19: Small ribosomal subunit protein eS6A
+分子 #20: 40S ribosomal protein S7-A
+分子 #21: 40S ribosomal protein S8
+分子 #22: Small ribosomal subunit protein uS4A
+分子 #23: Small ribosomal subunit protein uS17A
+分子 #24: 40S ribosomal protein S13
+分子 #25: 40S ribosomal protein S16-A
+分子 #26: ES17
+分子 #27: 40S ribosomal protein S19-A
+分子 #28: Small ribosomal subunit protein eS21A
+分子 #29: RPS22A isoform 1
+分子 #30: 40S ribosomal protein S23-A
+分子 #31: 40S ribosomal protein S24-A
+分子 #32: RPS26B isoform 1
+分子 #33: 40S ribosomal protein S27-A
+分子 #34: RPS29A isoform 1
+分子 #35: 40S ribosomal protein S30-A
+分子 #36: Small ribosomal subunit protein RACK1
+分子 #37: 60S ribosomal protein L2-A
+分子 #38: 60S ribosomal protein L3
+分子 #39: RPL4A isoform 1
+分子 #40: RPL5 isoform 1
+分子 #41: 60S ribosomal protein L6-A
+分子 #42: 60S ribosomal protein L7-A
+分子 #43: 60S ribosomal protein L8-A
+分子 #44: RPL9A isoform 1
+分子 #45: RPL10 isoform 1
+分子 #46: RPL11B isoform 1
+分子 #47: 60S ribosomal protein L13-A
+分子 #48: 60S ribosomal protein L14-A
+分子 #49: Ribosomal protein L15
+分子 #50: 60S ribosomal protein L16-A
+分子 #51: 60S ribosomal protein L17-A
+分子 #52: 60S ribosomal protein L18-A
+分子 #53: 60S ribosomal protein L19-A
+分子 #54: 60S ribosomal protein L20-A
+分子 #55: 60S ribosomal protein L21-A
+分子 #56: 60S ribosomal protein L22-A
+分子 #57: 60S ribosomal protein L23-A
+分子 #58: RPL24A isoform 1
+分子 #59: 60S ribosomal protein L25
+分子 #60: Large ribosomal subunit protein uL24A
+分子 #61: 60S ribosomal protein L27-A
+分子 #62: 60S ribosomal protein L28
+分子 #63: 60S ribosomal protein L29
+分子 #64: 60S ribosomal protein L30
+分子 #65: 60S ribosomal protein L31-A
+分子 #66: RPL32 isoform 1
+分子 #67: 60S ribosomal protein L33-A
+分子 #68: Large ribosomal subunit protein eL34A
+分子 #69: 60S ribosomal protein L35-A
+分子 #70: 60S ribosomal protein L36-A
+分子 #71: Large ribosomal subunit protein eL37A
+分子 #72: RPL38 isoform 1
+分子 #73: 60S ribosomal protein L39
+分子 #74: 60S ribosomal protein L40-A
+分子 #75: Large ribosomal subunit protein eL41B
+分子 #76: 60S ribosomal protein L42-A
+分子 #77: 60S ribosomal protein L43-A
+分子 #78: STM1 isoform 1
+分子 #79: Eukaryotic translation initiation factor 5A
+分子 #80: Small ribosomal subunit protein eS4A
+分子 #81: RPS31 isoform 1
+分子 #11: 5S ribosomal RNA
+分子 #12: 5.8S ribosomal RNA
+分子 #13: 25S ribosomal RNA
+分子 #14: 18S ribosomal RNA
+分子 #82: MAGNESIUM ION
+分子 #83: POTASSIUM ION
+分子 #84: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
+分子 #85: SPERMIDINE
+分子 #86: ZINC ION
+分子 #87: water
-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 |
---|---|
グリッド | モデル: Quantifoil / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 支持フィルム - Film thickness: 300 / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE-PROPANE |
詳細 | 80S peak from Sucrose gradient |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) 検出モード: COUNTING / 平均電子線量: 32.0 e/Å2 |
電子線 | 加速電圧: 200 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 / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 0.6 µm |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT / 当てはまり具合の基準: Correlation coefficient |
---|---|
得られたモデル | PDB-8bn3: |