+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 regulation of G1 to G0 transition / exit from mitosis / 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 / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition ...regulation of G1 to G0 transition / exit from mitosis / 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 / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / 90S preribosome / T cell proliferation involved in immune response / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / gastrulation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / glucose homeostasis / ribosome binding / retina development in camera-type eye / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / Golgi apparatus / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 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 |
-検証レポート
文書・要旨 | emd_0098_validation.pdf.gz | 404.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_0098_full_validation.pdf.gz | 404 KB | 表示 | |
XML形式データ | emd_0098_validation.xml.gz | 7.5 KB | 表示 | |
CIF形式データ | emd_0098_validation.cif.gz | 8.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0098 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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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 |
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: Tecnai Polara / 画像提供: FEI Company |
+画像解析
-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: |