+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8jdm | ||||||||||||
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タイトル | Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (rotated state) | ||||||||||||
要素 |
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キーワード | RIBOSOME / tRNA modifications / decoding | ||||||||||||
機能・相同性 | 機能・相同性情報 eukaryotic 80S initiation complex / : / negative regulation of protein neddylation / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / ribosomal protein import into nucleus ...eukaryotic 80S initiation complex / : / negative regulation of protein neddylation / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / ribosomal protein import into nucleus / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / oxidized purine DNA binding / neural crest cell differentiation / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / A band / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of G1 to G0 transition / exit from mitosis / laminin receptor activity / pigmentation / 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 / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / optic nerve development / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / retinal ganglion cell axon guidance / fibroblast growth factor binding / mammalian oogenesis stage / homeostatic process / positive regulation of mitochondrial depolarization / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / negative regulation of Wnt signaling pathway / lung morphogenesis / negative regulation of peptidyl-serine phosphorylation / iron-sulfur cluster binding / positive regulation of activated T cell proliferation / monocyte chemotaxis / male meiosis I / Protein hydroxylation / regulation of cell division / BH3 domain binding / cysteine-type endopeptidase activator activity involved in apoptotic process / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein localization to nucleus / 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 / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / positive regulation of cell cycle 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
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: 2.67 Å | ||||||||||||
データ登録者 | Ishiguro, K. / Yokoyama, T. / Shirouzu, M. / Suzuki, T. | ||||||||||||
資金援助 | 日本, 3件
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引用 | ジャーナル: Cell / 年: 2023 タイトル: Glycosylated queuosines in tRNAs optimize translational rate and post-embryonic growth. 著者: Xuewei Zhao / Ding Ma / Kensuke Ishiguro / Hironori Saito / Shinichiro Akichika / Ikuya Matsuzawa / Mari Mito / Toru Irie / Kota Ishibashi / Kimi Wakabayashi / Yuriko Sakaguchi / Takeshi ...著者: Xuewei Zhao / Ding Ma / Kensuke Ishiguro / Hironori Saito / Shinichiro Akichika / Ikuya Matsuzawa / Mari Mito / Toru Irie / Kota Ishibashi / Kimi Wakabayashi / Yuriko Sakaguchi / Takeshi Yokoyama / Yuichiro Mishima / Mikako Shirouzu / Shintaro Iwasaki / Takeo Suzuki / Tsutomu Suzuki / 要旨: Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further ...Transfer RNA (tRNA) modifications are critical for protein synthesis. Queuosine (Q), a 7-deaza-guanosine derivative, is present in tRNA anticodons. In vertebrate tRNAs for Tyr and Asp, Q is further glycosylated with galactose and mannose to generate galQ and manQ, respectively. However, biogenesis and physiological relevance of Q-glycosylation remain poorly understood. Here, we biochemically identified two RNA glycosylases, QTGAL and QTMAN, and successfully reconstituted Q-glycosylation of tRNAs using nucleotide diphosphate sugars. Ribosome profiling of knockout cells revealed that Q-glycosylation slowed down elongation at cognate codons, UAC and GAC (GAU), respectively. We also found that galactosylation of Q suppresses stop codon readthrough. Moreover, protein aggregates increased in cells lacking Q-glycosylation, indicating that Q-glycosylation contributes to proteostasis. Cryo-EM of human ribosome-tRNA complex revealed the molecular basis of codon recognition regulated by Q-glycosylations. Furthermore, zebrafish qtgal and qtman knockout lines displayed shortened body length, implying that Q-glycosylation is required for post-embryonic growth in vertebrates. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8jdm.cif.gz | 5.4 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8jdm.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8jdm.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
文書・要旨 | 8jdm_validation.pdf.gz | 2.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8jdm_full_validation.pdf.gz | 2.5 MB | 表示 | |
XML形式データ | 8jdm_validation.xml.gz | 366.3 KB | 表示 | |
CIF形式データ | 8jdm_validation.cif.gz | 609.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jd/8jdm ftp://data.pdbj.org/pub/pdb/validation_reports/jd/8jdm | HTTPS FTP |
-関連構造データ
関連構造データ | 36181MC 7y7cC 7y7dC 7y7eC 7y7fC 7y7gC 7y7hC 8jdjC 8jdkC 8jdlC 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 | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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非結晶学的対称性 (NCS) | NCS oper: (Code: givenMatrix: (0.820877854681, -0.561053033722, 0.106672588073), (0.469029170439, 0.768863938772, 0.43458012027), (-0.325839201098, -0.306704641321, 0.894293619579)ベクター: 95. ...NCS oper: (Code: given Matrix: (0.820877854681, -0.561053033722, 0.106672588073), ベクター: |
-要素
-RNA鎖 , 6種, 7分子 ABCDEFw
#1: RNA鎖 | 分子量: 4333.523 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) | ||||||||
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#2: RNA鎖 | 分子量: 24891.119 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) #3: RNA鎖 | | 分子量: 1641079.625 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA #4: RNA鎖 | | 分子量: 38691.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA / 参照: GenBank: NR_023363 #5: RNA鎖 | | 分子量: 50157.676 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA #48: RNA鎖 | | 分子量: 603528.062 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA |
+60S ribosomal protein ... , 41種, 41分子 GHIJKLMNOPQRSTUVWXYZabcdefghij...
-タンパク質 , 2種, 2分子 rAR
#43: タンパク質 | 分子量: 14758.394 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA / 参照: UniProt: P62987 |
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#79: タンパク質 | 分子量: 35115.652 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 細胞株: HELA / 参照: UniProt: P63244 |
+40S ribosomal protein ... , 30種, 30分子 xyz0123456789AAABACADAEAFAGAHAIAJAKALAMANAOAPAQ
-糖 , 1種, 2分子
#80: 糖 |
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-非ポリマー , 2種, 526分子
#81: 化合物 | ChemComp-MG / #82: 化合物 | ChemComp-ZN / |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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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: The complex of Human 80S Ribosome with mRNA and A-, P- site tRNA (rotated state) タイプ: COMPLEX 詳細: human 80S ribosome was incubated with mRNA and human cytoplasmic tRNA-Tyr Entity ID: #1, #3-#79 / 由来: NATURAL | ||||||||||||||||||||
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分子量 | 実験値: NO | ||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) / 株: HELA | ||||||||||||||||||||
緩衝液 | pH: 7.4 / 詳細: The Buffer pH was adjusted to 7.4 using KOH. | ||||||||||||||||||||
緩衝液成分 |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: 24nM ribosomes were incubated with 500nM tRNA and mRNA | ||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 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 / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 500 nm |
撮影 | 平均露光時間: 1 sec. / 電子線照射量: 50 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 2 / 実像数: 32000 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 548386 | ||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.67 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 75250 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 67.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
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