+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0098 | ||||||||||||
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タイトル | tRNA translocation by the eukaryotic 80S ribosome and the impact of GTP hydrolysis, Translocation-intermediate-POST-1 (TI-POST-1) | ||||||||||||
マップデータ | |||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 ribosomal subunit / regulation of G1 to G0 transition / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition ...ribosomal subunit / regulation of G1 to G0 transition / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / positive regulation of mitochondrial depolarization / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / translation regulator activity / cellular response to actinomycin D / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 小胞体 / gastrulation / signaling adaptor activity / rescue of stalled ribosome / negative regulation of smoothened signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / negative regulation of peptidyl-serine phosphorylation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cytosolic ribosome / positive regulation of intrinsic apoptotic signaling pathway / ribosomal large subunit biogenesis / small-subunit processome / SH2 domain binding / cyclin binding / positive regulation of translation / protein kinase C binding / : / cellular response to glucose stimulus / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / mRNA 5'-UTR binding / ribosomal small subunit biogenesis / transcription coactivator binding / negative regulation of cell growth / receptor tyrosine kinase binding / cellular response to growth factor stimulus / rRNA processing / positive regulation of canonical Wnt signaling pathway / cytosolic small ribosomal subunit / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / ribosome binding / cytosolic large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / midbody / protein phosphatase binding / 細胞分化 / リボソーム / protein stabilization / rRNA binding / protein ubiquitination / regulation of cell cycle / structural constituent of ribosome / positive regulation of cell migration / 翻訳 (生物学) / ribonucleoprotein complex / positive regulation of protein phosphorylation / negative regulation of gene expression / 中心体 / シナプス / ubiquitin protein ligase binding / positive regulation of cell population proliferation / 核小体 / positive regulation of gene expression / perinuclear region of cytoplasm / ゴルジ体 / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / ミトコンドリア / RNA binding / zinc ion binding / 核質 / metal ion binding / 細胞質基質 類似検索 - 分子機能 | ||||||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Enterobacteria phage SP6 (ファージ) / Saccharomyces cerevisiae (パン酵母) / Rabbit (ウサギ) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | ||||||||||||
データ登録者 | Flis J / Holm M / Rundlet EJ / Loerke J / Hilal T / Dabrowski M / Buerger J / Mielke T / Blanchard SC / Spahn CMT / Budkevich TV | ||||||||||||
資金援助 | ドイツ, 米国, 3件
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引用 | ジャーナル: Cell Rep / 年: 2018 タイトル: tRNA Translocation by the Eukaryotic 80S Ribosome and the Impact of GTP Hydrolysis. 著者: Julia Flis / Mikael Holm / Emily J Rundlet / Justus Loerke / Tarek Hilal / Marylena Dabrowski / Jörg Bürger / Thorsten Mielke / Scott C Blanchard / Christian M T Spahn / Tatyana V Budkevich / 要旨: Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes ...Translocation moves the tRNA⋅mRNA module directionally through the ribosome during the elongation phase of protein synthesis. Although translocation is known to entail large conformational changes within both the ribosome and tRNA substrates, the orchestrated events that ensure the speed and fidelity of this critical aspect of the protein synthesis mechanism have not been fully elucidated. Here, we present three high-resolution structures of intermediates of translocation on the mammalian ribosome where, in contrast to bacteria, ribosomal complexes containing the translocase eEF2 and the complete tRNA⋅mRNA module are trapped by the non-hydrolyzable GTP analog GMPPNP. Consistent with the observed structures, single-molecule imaging revealed that GTP hydrolysis principally facilitates rate-limiting, final steps of translocation, which are required for factor dissociation and which are differentially regulated in bacterial and mammalian systems by the rates of deacyl-tRNA dissociation from the E site. | ||||||||||||
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_0098.map.gz | 230.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0098-v30.xml emd-0098.xml | 105.4 KB 105.4 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0098.png | 72.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0098 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0098 | 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_0098.map.gz / 形式: CCP4 / 大きさ: 253.4 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: 0.975 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 : translocation intermediate TI-POST-1
+超分子 #1: translocation intermediate TI-POST-1
+超分子 #2: Ribosome
+超分子 #3: mRNA
+超分子 #4: tRNA
+分子 #1: 28S ribosomal RNA
+分子 #2: ap/P-site tRNA
+分子 #3: mRNA
+分子 #4: pe/E-site-tRNA
+分子 #5: 18S ribosomal RNA
+分子 #39: 5.8S ribosomal RNA
+分子 #40: 5S ribosomal RNA
+分子 #6: ribosomal protein uS3
+分子 #7: Ribosomal protein S5
+分子 #8: ribosomal protein eS10
+分子 #9: 40S ribosomal protein S12
+分子 #10: ribosomal protein uS19
+分子 #11: ribosomal protein uS9
+分子 #12: ribosomal protein eS17
+分子 #13: ribosomal protein uS13
+分子 #14: ribosomal protein eS19
+分子 #15: ribosomal protein uS10
+分子 #16: ribosomal protein eS25
+分子 #17: Ribosomal protein S28
+分子 #18: ribosomal protein uS14
+分子 #19: Ribosomal protein S27a
+分子 #20: ribosomal protein RACK 1
+分子 #21: ribosomal protein uS2
+分子 #22: 40S ribosomal protein S3a
+分子 #23: ribosomal protein uS5
+分子 #24: ribosomal protein eS4
+分子 #25: 40S ribosomal protein S6
+分子 #26: 40S ribosomal protein S7
+分子 #27: ribosomal protein eS8
+分子 #28: Ribosomal protein S9 (Predicted)
+分子 #29: Ribosomal protein S11
+分子 #30: ribosomal protein uS15
+分子 #31: ribosomal protein uS11
+分子 #32: ribosomal protein eS21
+分子 #33: Ribosomal protein S15a
+分子 #34: Ribosomal protein S23
+分子 #35: ribosomal protein eS24
+分子 #36: ribosomal protein eS26
+分子 #37: ribosomal protein eS27
+分子 #38: ribosomal protein eS30
+分子 #41: Ribosomal protein L8
+分子 #42: ribosomal protein uL3
+分子 #43: ribosomal protein uL4
+分子 #44: ribosomal protein uL18
+分子 #45: ribosomal protein eL6
+分子 #46: ribosomal protein uL30
+分子 #47: ribosomal protein eL8
+分子 #48: ribosomal protein uL6
+分子 #49: Ribosomal protein L10 (Predicted)
+分子 #50: Ribosomal protein L11
+分子 #51: ribosomal protein eL13
+分子 #52: ribosomal protein eL14
+分子 #53: Ribosomal protein L15
+分子 #54: ribosomal protein uL13
+分子 #55: ribosomal protein uL22
+分子 #56: ribosomal protein eL18
+分子 #57: ribosomal protein eL19
+分子 #58: ribosomal protein eL20
+分子 #59: ribosomal protein eL21
+分子 #60: ribosomal protein eL22
+分子 #61: Ribosomal protein L23
+分子 #62: ribosomal protein eL24
+分子 #63: ribosomal protein uL23
+分子 #64: Ribosomal protein L26
+分子 #65: 60S ribosomal protein L27
+分子 #66: ribosomal protein uL15
+分子 #67: ribosomal protein eL29
+分子 #68: ribosomal protein eL30
+分子 #69: ribosomal protein eL31
+分子 #70: ribosomal protein eL32
+分子 #71: ribosomal protein eL33
+分子 #72: ribosomal protein eL34
+分子 #73: ribosomal protein uL29
+分子 #74: ribosomal protein eL36
+分子 #75: Ribosomal protein L37
+分子 #76: ribosomal protein eL38
+分子 #77: ribosomal protein eL39
+分子 #78: ribosomal protein eL40
+分子 #79: ribosomal protein eL41
+分子 #80: ribosomal protein eL42
+分子 #81: ribosomal protein eL43
+分子 #82: ribosomal protein eL28
+分子 #83: Ribosomal protein
+分子 #84: Ribosomal protein L12
+分子 #85: ribosomal protein uL10
+分子 #86: eukaryotic elongation factor 2 (eEF2)
+分子 #87: MAGNESIUM ION
+分子 #88: ZINC ION
+分子 #89: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
-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 POLARA 300 |
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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 FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均露光時間: 5.0 sec. / 平均電子線量: 30.0 e/Å2 |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 270000 |
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初期モデル | モデルのタイプ: OTHER / 詳細: filtered empty 80S |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 32386 |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-6gz3: |