+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12977 | |||||||||
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タイトル | Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / RNA polymerase transcription factor SL1 complex / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly ...RNA polymerase I core factor complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / RNA polymerase transcription factor SL1 complex / RNA polymerase I core promoter sequence-specific DNA binding / protein kinase regulator activity / nucleolar large rRNA transcription by RNA polymerase I / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / translation elongation factor 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) / 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) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-translational protein modification / maturation of LSU-rRNA / ribosomal large subunit biogenesis / methyltransferase activity / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / rRNA processing / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / methylation / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / zinc ion binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Chaetomium thermophilum var. thermophilum DSM 1495 (菌類) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.0 Å | |||||||||
データ登録者 | Kisonaite M / Wild K / Sinning I | |||||||||
資金援助 | ドイツ, 1件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation. 著者: Miglė Kišonaitė / Klemens Wild / Karine Lapouge / Thomas Ruppert / Irmgard Sinning / 要旨: Ribosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from ...Ribosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from a thermophilic fungus in two rotational states, which due to increased 80S stability provide a number of mechanistic details of eukaryotic translation. We identify a universally conserved 'nested base-triple knot' in the 26S rRNA at the polypeptide tunnel exit with a bulged-out nucleotide that likely serves as an adaptable element for nascent chain containment and handover. We visualize the structure and dynamics of the ribosome protective factor Stm1 upon ribosomal 40S head swiveling. We describe the structural impact of a unique and essential macp Ψ 18S rRNA hyper-modification embracing the anticodon wobble-position for eukaryotic tRNA and mRNA translocation. We complete the eEF2-GTPase switch cycle describing the GDP-bound post-hydrolysis state. Taken together, our data and their integration into the structural landscape of 80S ribosomes furthers our understanding of protein biogenesis. | |||||||||
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_12977.map.gz | 174.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12977-v30.xml emd-12977.xml | 100.8 KB 100.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12977_fsc.xml | 21.7 KB | 表示 | FSCデータファイル |
画像 | emd_12977.png | 193.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12977 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12977 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12977_validation.pdf.gz | 385.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12977_full_validation.pdf.gz | 384.7 KB | 表示 | |
XML形式データ | emd_12977_validation.xml.gz | 16.1 KB | 表示 | |
CIF形式データ | emd_12977_validation.cif.gz | 21.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12977 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12977 | 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_12977.map.gz / 形式: CCP4 / 大きさ: 437.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.1 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 : Chaetomium thermophilum 80S ribosome
+超分子 #1: Chaetomium thermophilum 80S ribosome
+分子 #1: 26S rRNA
+分子 #2: 18S rRNA
+分子 #3: 5S rRNA
+分子 #4: 5.8S rRNA
+分子 #5: pe/E tRNA
+分子 #6: Putative guanine nucleotide-binding protein
+分子 #7: HABP4_PAI-RBP1 domain-containing protein
+分子 #8: Elongation factor 2
+分子 #9: 60S ribosomal protein L2-like protein
+分子 #10: 60S ribosomal protein L3-like protein
+分子 #11: 60S ribosomal protein L4-like protein
+分子 #12: 60S ribosomal protein l5-like protein
+分子 #13: 60S ribosomal protein L6
+分子 #14: 60S ribosomal protein l7-like protein
+分子 #15: 60S ribosomal protein L8
+分子 #16: 60S ribosomal protein l9-like protein
+分子 #17: 60S ribosomal protein L10-like protein
+分子 #18: Putative ribosomal protein
+分子 #19: 60S ribosomal protein L12-like protein
+分子 #20: 60S ribosomal protein L13
+分子 #21: 60S ribosomal protein L14-like protein
+分子 #22: Ribosomal protein L15
+分子 #23: 60S ribosomal protein L16-like protein
+分子 #24: 60S ribosomal protein l17-like protein
+分子 #25: Ribosomal protein L18-like protein
+分子 #26: Ribosomal protein L19
+分子 #27: 60S ribosomal protein L20
+分子 #28: 60S ribosomal protein l21-like protein
+分子 #29: 60S ribosomal protein L22-like protein
+分子 #30: 60S ribosomal protein l23-like protein
+分子 #31: 60S ribosomal protein L24-like protein
+分子 #32: 60S ribosomal protein L25-like protein
+分子 #33: 60S ribosomal protein L26-like protein
+分子 #34: 60S ribosomal protein L27
+分子 #35: 60S ribosomal protein L28-like protein
+分子 #36: 60S ribosomal protein L29
+分子 #37: 60S ribosomal protein l30-like protein
+分子 #38: Putative 60S ribosomal protein
+分子 #39: 60S ribosomal protein L32-like protein
+分子 #40: 60S ribosomal protein l33-like protein
+分子 #41: Ribosomal protein l34-like protein
+分子 #42: Dolichyl-diphosphooligosaccharide--protein glycotransferase
+分子 #43: 60S ribosomal protein L36
+分子 #44: Ribosomal protein L37
+分子 #45: 60S ribosomal protein L38-like protein
+分子 #46: Ribosomal protein eL39
+分子 #47: Ubiquitin
+分子 #48: 60S ribosomal protein L41-A
+分子 #49: 60S ribosomal protein L44-like protein
+分子 #50: 60S ribosomal protein L43-like protein
+分子 #51: Putative 60S ribosomal protein
+分子 #52: 60S acidic ribosomal protein P0
+分子 #53: 40S ribosomal protein S0
+分子 #54: 40S ribosomal protein S1
+分子 #55: 40S ribosomal protein S2-like protein
+分子 #56: 40S ribosomal protein S3-like protein
+分子 #57: 40S ribosomal protein S4
+分子 #58: 40S ribosomal protein s5-like protein
+分子 #59: 40S ribosomal protein S6
+分子 #60: 40S ribosomal protein S7
+分子 #61: 40S ribosomal protein S8
+分子 #62: 40S ribosomal protein s9-like protein
+分子 #63: 40S ribosomal protein s10-like protein
+分子 #64: 40S ribosomal protein S11-like protein
+分子 #65: 40S ribosomal protein S12
+分子 #66: 40S ribosomal protein S13-like protein
+分子 #67: 40S ribosomal protein S14-like protein
+分子 #68: 40S ribosomal protein s15-like protein
+分子 #69: 40S ribosomal protein S16-like protein
+分子 #70: 40S ribosomal protein S17-like protein
+分子 #71: Putative ribosomal protein
+分子 #72: 40S ribosomal protein S19-like protein
+分子 #73: 40S ribosomal protein S20-like protein
+分子 #74: 40S ribosomal protein S21-like protein
+分子 #75: 40S ribosomal protein S22-like protein
+分子 #76: 40S ribosomal protein s23-like protein
+分子 #77: 40S ribosomal protein S24
+分子 #78: 40S ribosomal protein S25
+分子 #79: 40S ribosomal protein S26
+分子 #80: Ribosomal protein s27-like protein
+分子 #81: 40S ribosomal protein S28-like protein
+分子 #82: Ribosomal protein uS14
+分子 #83: 40S ribosomal protein S30
+分子 #84: 40S ribosomal protein S27a-like protein
+分子 #85: MAGNESIUM ION
+分子 #86: GUANOSINE-5'-DIPHOSPHATE
+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 QUANTUM (4k x 4k) 平均電子線量: 32.51 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 |