+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-28635 | |||||||||
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タイトル | Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II | |||||||||
マップデータ | Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II | |||||||||
試料 |
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キーワード | rRNA pseudouridylation / IRES initiation / confomation / eEF2 / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / ribosomal subunit / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / hexon binding / pre-mRNA 5'-splice site binding / 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 / protein-RNA complex assembly / translation elongation factor activity / ribosomal subunit export from nucleus / translation regulator activity / 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) / maturation of LSU-rRNA / Neutrophil degranulation / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / translational initiation / macroautophagy / protein kinase C binding / positive regulation of apoptotic signaling pathway / 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 / ribosome biogenesis / viral capsid / ribosome binding / ribosomal small subunit assembly / protein-folding chaperone binding / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / ribonucleoprotein complex / translation / negative regulation of gene expression / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase binding / host cell nucleus / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / 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: 2.62 Å | |||||||||
データ登録者 | Zhao Y / Rai J / Li H | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Sci Adv / 年: 2023 タイトル: Regulation of translation by ribosomal RNA pseudouridylation. 著者: Yu Zhao / Jay Rai / Hong Li / 要旨: Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such ...Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes. | |||||||||
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_28635.map.gz | 230 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-28635-v30.xml emd-28635.xml | 103.6 KB 103.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_28635.png | 121.1 KB | ||
Filedesc metadata | emd-28635.cif.gz | 20.3 KB | ||
その他 | emd_28635_half_map_1.map.gz emd_28635_half_map_2.map.gz | 226.5 MB 226.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-28635 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28635 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_28635_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_28635_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_28635_validation.xml.gz | 16.2 KB | 表示 | |
CIF形式データ | emd_28635_validation.cif.gz | 19.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28635 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28635 | HTTPS FTP |
-関連構造データ
関連構造データ | 8evsMC 8eubC 8evpC 8evqC 8evrC 8evtC 8ewbC 8ewcC 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) |
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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_28635.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome entry site (IRES), eEF2 and GDP, Structure II | ||||||||||||||||||||||||||||||||||||
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: 1.06 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
-ハーフマップ: Half Map 1
ファイル | emd_28635_half_map_1.map | ||||||||||||
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注釈 | Half Map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half Map 2
ファイル | emd_28635_half_map_2.map | ||||||||||||
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注釈 | Half Map 2 | ||||||||||||
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 : Hypopseudouridylated ribosome with TSV IRES, eEF2 and GDP
+超分子 #1: Hypopseudouridylated ribosome with TSV IRES, eEF2 and GDP
+分子 #1: 40S ribosomal protein S0-A
+分子 #2: RPS1A isoform 1
+分子 #3: RPS2 isoform 1
+分子 #4: 40S ribosomal protein S4-A
+分子 #5: 40S ribosomal protein S6-A
+分子 #6: 40S ribosomal protein S7-A
+分子 #7: 40S ribosomal protein S8-A
+分子 #8: 40S ribosomal protein S9-A
+分子 #9: 40S ribosomal protein S11-A
+分子 #10: 40S ribosomal protein S13
+分子 #11: 40S ribosomal protein S14-A
+分子 #12: 40S ribosomal protein S21-A
+分子 #13: RPS22A isoform 1
+分子 #14: 40S ribosomal protein S23-A
+分子 #15: 40S ribosomal protein S24-A
+分子 #16: RPS26B isoform 1
+分子 #17: 40S ribosomal protein S27-A
+分子 #18: 40S ribosomal protein S30-A
+分子 #19: RPS3 isoform 1
+分子 #20: Rps5p
+分子 #21: 40S ribosomal protein S10-A
+分子 #22: RPS15 isoform 1
+分子 #23: 40S ribosomal protein S16-A
+分子 #24: 40S ribosomal protein S17-A
+分子 #25: 40S ribosomal protein S18-A
+分子 #26: 40S ribosomal protein S19-A
+分子 #27: RPS20 isoform 1
+分子 #28: RPS25A isoform 1
+分子 #29: RPS28A isoform 1
+分子 #30: RPS29A isoform 1
+分子 #31: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #32: Ubiquitin-40S ribosomal protein S31
+分子 #33: 40S ribosomal protein S12
+分子 #35: 60S ribosomal protein L2-A
+分子 #36: 60S ribosomal protein L3
+分子 #37: RPL4A isoform 1
+分子 #41: RPL5 isoform 1
+分子 #42: 60S ribosomal protein L6-A
+分子 #43: 60S ribosomal protein L7-A
+分子 #44: 60S ribosomal protein L8-A
+分子 #45: 60S ribosomal protein L9-A
+分子 #46: RPL10 isoform 1
+分子 #47: RPL11A isoform 1
+分子 #48: 60S ribosomal protein L13-A
+分子 #49: 60S ribosomal protein L14-A
+分子 #50: 60S ribosomal protein L15-A
+分子 #51: 60S ribosomal protein L16-A
+分子 #52: 60S ribosomal protein L17-A
+分子 #53: 60S ribosomal protein L18-A
+分子 #54: 60S ribosomal protein L19-A
+分子 #55: 60S ribosomal protein L20
+分子 #56: 60S ribosomal protein L21-A
+分子 #57: 60S ribosomal protein L22-A
+分子 #58: 60S ribosomal protein L23-A
+分子 #59: RPL24A isoform 1
+分子 #60: 60S ribosomal protein L25
+分子 #61: 60S ribosomal protein L26-A
+分子 #62: 60S ribosomal protein L27-A
+分子 #63: 60S ribosomal protein L28
+分子 #64: RPL29 isoform 1
+分子 #65: 60S ribosomal protein L30
+分子 #66: 60S ribosomal protein L31-A
+分子 #67: RPL32 isoform 1
+分子 #68: 60S ribosomal protein L33-A
+分子 #69: 60S ribosomal protein L34-A
+分子 #70: 60S ribosomal protein L35-A
+分子 #71: 60S ribosomal protein L36-A
+分子 #72: 60S ribosomal protein L37-A
+分子 #73: RPL38 isoform 1
+分子 #74: 60S ribosomal protein L39
+分子 #75: Ubiquitin-60S ribosomal protein L40
+分子 #76: 60S ribosomal protein L41-A
+分子 #77: 60S ribosomal protein L42-A
+分子 #78: 60S ribosomal protein L43-A
+分子 #79: RPL1A isoform 1
+分子 #80: Elongation factor 2
+分子 #81: 60S acidic ribosomal protein P0
+分子 #34: 18S rRNA
+分子 #38: 25S rRNA
+分子 #39: 5s rRNA
+分子 #40: 5.8 S rRNA
+分子 #82: TSV IRES
+分子 #83: MAGNESIUM ION
+分子 #84: ZINC ION
+分子 #85: GUANOSINE-5'-DIPHOSPHATE
-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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糖包埋 | 材質: carbon |
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 K3 BIOQUANTUM (6k x 4k) 平均電子線量: 60.0 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 / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.0 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: PDB ENTRY PDBモデル - PDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.62 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 65607 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |