+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-36179 | ||||||||||||
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タイトル | Structure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU) | ||||||||||||
マップデータ | |||||||||||||
試料 |
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キーワード | tRNA modifications / decoding / RIBOSOME | ||||||||||||
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 / TORC2 complex binding / negative regulation of RNA splicing / negative regulation of DNA repair / 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 / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / negative regulation of phagocytosis / 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 / 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 / pigmentation / protein kinase A binding / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / 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 / mammalian oogenesis stage / fibroblast growth factor binding / homeostatic process / positive regulation of mitochondrial depolarization / G1 to G0 transition / activation-induced cell death of T cells / macrophage chemotaxis / positive regulation of T cell receptor signaling pathway / lung morphogenesis / negative regulation of peptidyl-serine phosphorylation / iron-sulfur cluster binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / male meiosis I / monocyte chemotaxis / 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 / protein localization to nucleus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.26 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
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_36179.map.gz | 525.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-36179-v30.xml emd-36179.xml | 103.9 KB 103.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_36179_fsc.xml | 18.6 KB | 表示 | FSCデータファイル |
画像 | emd_36179.png | 78.5 KB | ||
Filedesc metadata | emd-36179.cif.gz | 21.3 KB | ||
その他 | emd_36179_additional_1.map.gz emd_36179_half_map_1.map.gz emd_36179_half_map_2.map.gz | 455.1 MB 456.5 MB 456.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-36179 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36179 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_36179_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_36179_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_36179_validation.xml.gz | 26.2 KB | 表示 | |
CIF形式データ | emd_36179_validation.cif.gz | 35 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36179 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36179 | HTTPS FTP |
-関連構造データ
関連構造データ | 8jdkMC 7y7cC 7y7dC 7y7eC 7y7fC 7y7gC 7y7hC 8jdjC 8jdlC 8jdmC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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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
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_36179.map.gz / 形式: CCP4 / 大きさ: 567.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.83 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: before postprocess
ファイル | emd_36179_additional_1.map | ||||||||||||
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注釈 | before postprocess | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_36179_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_36179_half_map_2.map | ||||||||||||
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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 : The complex of Human 80S Ribosome with mRNA and A-, P- site tRNA
+超分子 #1: The complex of Human 80S Ribosome with mRNA and A-, P- site tRNA
+分子 #1: mRNA
+分子 #2: tRNA (Asp)
+分子 #3: 28S ribosomal RNA
+分子 #4: 5S ribosomal RNA
+分子 #5: 5.8S ribosomal RNA
+分子 #48: 18S ribosomal RNA
+分子 #6: 60S ribosomal protein L8
+分子 #7: 60S ribosomal protein L3
+分子 #8: 60S ribosomal protein L4
+分子 #9: 60S ribosomal protein L5
+分子 #10: 60S ribosomal protein L6
+分子 #11: 60S ribosomal protein L7
+分子 #12: 60S ribosomal protein L7a
+分子 #13: 60S ribosomal protein L9
+分子 #14: 60S ribosomal protein L10-like
+分子 #15: 60S ribosomal protein L11
+分子 #16: 60S ribosomal protein L13
+分子 #17: 60S ribosomal protein L14
+分子 #18: 60S ribosomal protein L15
+分子 #19: 60S ribosomal protein L13a
+分子 #20: 60S ribosomal protein L17
+分子 #21: 60S ribosomal protein L18
+分子 #22: 60S ribosomal protein L19
+分子 #23: 60S ribosomal protein L18a
+分子 #24: 60S ribosomal protein L21
+分子 #25: 60S ribosomal protein L22
+分子 #26: 60S ribosomal protein L23
+分子 #27: 60S ribosomal protein L24
+分子 #28: 60S ribosomal protein L23a
+分子 #29: 60S ribosomal protein L26
+分子 #30: 60S ribosomal protein L27
+分子 #31: 60S ribosomal protein L27a
+分子 #32: 60S ribosomal protein L29
+分子 #33: 60S ribosomal protein L30
+分子 #34: 60S ribosomal protein L31
+分子 #35: 60S ribosomal protein L32
+分子 #36: 60S ribosomal protein L35a
+分子 #37: 60S ribosomal protein L34
+分子 #38: 60S ribosomal protein L35
+分子 #39: 60S ribosomal protein L36
+分子 #40: 60S ribosomal protein L37
+分子 #41: 60S ribosomal protein L38
+分子 #42: 60S ribosomal protein L39
+分子 #43: Ubiquitin-60S ribosomal protein L40
+分子 #44: 60S ribosomal protein L41
+分子 #45: 60S ribosomal protein L36a
+分子 #46: 60S ribosomal protein L37a
+分子 #47: 60S ribosomal protein L28
+分子 #49: 40S ribosomal protein SA
+分子 #50: 40S ribosomal protein S3a
+分子 #51: 40S ribosomal protein S2
+分子 #52: 40S ribosomal protein S3
+分子 #53: 40S ribosomal protein S4, X isoform
+分子 #54: 40S ribosomal protein S5
+分子 #55: 40S ribosomal protein S6
+分子 #56: 40S ribosomal protein S7
+分子 #57: 40S ribosomal protein S8
+分子 #58: 40S ribosomal protein S9
+分子 #59: 40S ribosomal protein S10
+分子 #60: 40S ribosomal protein S11
+分子 #61: 40S ribosomal protein S13
+分子 #62: 40S ribosomal protein S14
+分子 #63: 40S ribosomal protein S15
+分子 #64: 40S ribosomal protein S16
+分子 #65: 40S ribosomal protein S17
+分子 #66: 40S ribosomal protein S18
+分子 #67: 40S ribosomal protein S19
+分子 #68: 40S ribosomal protein S20
+分子 #69: 40S ribosomal protein S21
+分子 #70: 40S ribosomal protein S15a
+分子 #71: 40S ribosomal protein S23
+分子 #72: 40S ribosomal protein S24
+分子 #73: 40S ribosomal protein S25
+分子 #74: 40S ribosomal protein S26
+分子 #75: 40S ribosomal protein S27
+分子 #76: 40S ribosomal protein S28
+分子 #77: 40S ribosomal protein S29
+分子 #78: 40S ribosomal protein S30
+分子 #79: Receptor of activated protein C kinase 1
+分子 #80: MAGNESIUM ION
+分子 #81: alpha-D-mannopyranose
+分子 #82: ZINC ION
-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 構成要素:
詳細: The Buffer pH was adjusted to 7.4 using KOH. | ||||||||||||
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 10 sec. | ||||||||||||
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 IV | ||||||||||||
詳細 | 24nM ribosomes were incubated with 500nM tRNAs and mRNA |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | 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: 26000 / 平均電子線量: 50.0 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 / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 0.5 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |