+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6mtd | |||||||||
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タイトル | Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with 40S head swivel) | |||||||||
要素 |
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キーワード | RIBOSOME / translation | |||||||||
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 / 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 / protein kinase A binding / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / Ribosomal scanning and start codon recognition / organelle membrane / Translation initiation complex formation / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / 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 / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / 90S preribosome / T cell proliferation involved in immune response / protein-RNA complex assembly / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / erythrocyte development 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
データ登録者 | Brown, A. / Baird, M.R. / Yip, M.C.J. / 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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6mtd.cif.gz | 4.8 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6mtd.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6mtd.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/mt/6mtd ftp://data.pdbj.org/pub/pdb/validation_reports/mt/6mtd | HTTPS FTP |
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-関連構造データ
関連構造データ | 9240MC 9234C 9235C 9236C 9237C 9239C 9241C 9242C 6mtbC 6mtcC 6mteC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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-要素
-RNA鎖 , 4種, 4分子 5789
#1: RNA鎖 | 分子量: 1167366.125 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
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#2: RNA鎖 | 分子量: 38691.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: GenBank: 39 |
#3: RNA鎖 | 分子量: 48559.699 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
#51: RNA鎖 | 分子量: 548241.438 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
+タンパク質 , 77種, 77分子 ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-タンパク質・ペプチド , 3種, 3分子 lnw
#40: タンパク質・ペプチド | 分子量: 6324.579 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: UniProt: G1TTN1 |
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#42: タンパク質・ペプチド | 分子量: 3473.451 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
#50: タンパク質・ペプチド | 分子量: 3083.312 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
-非ポリマー , 3種, 306分子
#85: 化合物 | ChemComp-MG / #86: 化合物 | ChemComp-ZN / #87: 化合物 | ChemComp-GDP / | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Rabbit 80S ribosome with eEF2 and SERBP1 (unrotated state with head swivel) タイプ: RIBOSOME / Entity ID: #1-#84 / 由来: NATURAL |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) / 細胞内の位置: cytoplasm |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | Film material: CARBON |
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / Cs: 2.7 mm |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 1.1 sec. / 電子線照射量: 40 e/Å2 / 検出モード: INTEGRATING フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
画像スキャン | 動画フレーム数/画像: 17 / 利用したフレーム数/画像: 1-17 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 146801 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 5LZV |