+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9242 | |||||||||
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タイトル | Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state) | |||||||||
マップデータ | Postprocessed map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / 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) ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / 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) / : / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / 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) / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Formation of a pool of free 40S subunits / 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) / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / 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) / Separation of Sister Chromatids / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of endodeoxyribonuclease activity / : / negative regulation of DNA repair / TORC2 complex binding / oxidized purine DNA binding / supercoiled DNA binding / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein kinase A binding / Ribosomal scanning and start codon recognition / Translation initiation complex formation / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / SARS-CoV-1 modulates host translation machinery / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / organelle membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / 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) / 小胞体 / spindle assembly / MDM2/MDM4 family protein binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation initiation factor binding / maturation of SSU-rRNA / : / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of apoptotic signaling pathway / positive regulation of microtubule polymerization / positive regulation of JUN kinase activity / negative regulation of protein ubiquitination / Hsp70 protein binding / positive regulation of interleukin-2 production / DNA-(apurinic or apyrimidinic site) lyase 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Rabbit (ウサギ) / Bovine (ウシ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å | |||||||||
データ登録者 | Brown A / Baird MR / Yip MCJ / Murray J / Shao S | |||||||||
引用 | ジャーナル: Elife / 年: 2018 タイトル: Structures of translationally inactive mammalian ribosomes. 著者: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao / 要旨: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression. | |||||||||
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_9242.map.gz | 12.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9242-v30.xml emd-9242.xml | 97.6 KB 97.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_9242_fsc.xml | 14.1 KB | 表示 | FSCデータファイル |
画像 | emd_9242.png | 172 KB | ||
その他 | emd_9242_additional.map.gz emd_9242_half_map_1.map.gz emd_9242_half_map_2.map.gz | 214.2 MB 214.5 MB 214.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9242 | HTTPS FTP |
-関連構造データ
関連構造データ | 6mteMC 9234C 9235C 9236C 9237C 9239C 9240C 9241C 6mtbC 6mtcC 6mtdC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ |
-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_9242.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 | Postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.34 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
-追加マップ: Pre-postprocessed map
ファイル | emd_9242_additional.map | ||||||||||||
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注釈 | Pre-postprocessed map | ||||||||||||
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 1
ファイル | emd_9242_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_9242_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 : Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
+超分子 #1: Rabbit 80S ribosome with eEF2 and SERBP1 (rotated state)
+分子 #1: 28S rRNA
+分子 #2: 5S rRNA
+分子 #3: 5.8S rRNA
+分子 #50: 18S rRNA
+分子 #4: uL2
+分子 #5: uL3
+分子 #6: uL4
+分子 #7: uL18
+分子 #8: eL6
+分子 #9: uL30
+分子 #10: eL8
+分子 #11: uL6
+分子 #12: uL16
+分子 #13: uL5
+分子 #14: eL13
+分子 #15: eL14
+分子 #16: eL15
+分子 #17: uL13
+分子 #18: uL22
+分子 #19: eL18
+分子 #20: eL19
+分子 #21: eL20
+分子 #22: eL21
+分子 #23: eL22
+分子 #24: uL14
+分子 #25: eL24
+分子 #26: uL23
+分子 #27: uL24
+分子 #28: eL27
+分子 #29: uL15
+分子 #30: eL29
+分子 #31: eL30
+分子 #32: eL31
+分子 #33: eL32
+分子 #34: eL33
+分子 #35: eL34
+分子 #36: uL29
+分子 #37: eL36
+分子 #38: eL37
+分子 #39: eL38
+分子 #40: eL39
+分子 #41: eL40
+分子 #42: eL41
+分子 #43: eL42
+分子 #44: eL43
+分子 #45: eL28
+分子 #46: uL10
+分子 #47: uL11
+分子 #48: eEF2
+分子 #49: SERBP1
+分子 #51: uS2
+分子 #52: eS1
+分子 #53: uS5
+分子 #54: uS3
+分子 #55: eS4
+分子 #56: uS7
+分子 #57: eS6
+分子 #58: eS7
+分子 #59: eS8
+分子 #60: uS4
+分子 #61: eS10
+分子 #62: uS17
+分子 #63: eS12
+分子 #64: uS15
+分子 #65: uS11
+分子 #66: uS19
+分子 #67: uS9
+分子 #68: eS17
+分子 #69: uS13
+分子 #70: eS19
+分子 #71: uS10
+分子 #72: eS21
+分子 #73: uS8
+分子 #74: uS12
+分子 #75: eS24
+分子 #76: eS25
+分子 #77: eS26
+分子 #78: eS27
+分子 #79: eS28
+分子 #80: uS14
+分子 #81: eS30
+分子 #82: eS31
+分子 #83: RACK1
+分子 #84: MAGNESIUM ION
+分子 #85: ZINC ION
+分子 #86: 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: 7.4 |
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 5.0 nm |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK II |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 | 倍率(補正後): 104478 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - 画像ごとのフレーム数: 1-17 / 平均露光時間: 1.1 sec. / 平均電子線量: 40.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |