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データを開く
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基本情報
| 登録情報 | ![]() | ||||||||||||
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| タイトル | Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state) | ||||||||||||
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translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus ...translation at presynapse / exit from mitosis / optic nerve development / response to insecticide / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of ubiquitin-protein transferase activity / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / positive regulation of DNA-templated transcription initiation / alpha-beta T cell differentiation / TNFR1-mediated ceramide production / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / negative regulation of RNA splicing / TORC2 complex binding / neural crest cell differentiation / supercoiled DNA binding / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / cytoplasmic translational initiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / rRNA modification in the nucleus and cytosol / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / laminin receptor activity / protein kinase A binding / homeostatic process / pigmentation / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / macrophage chemotaxis / lung morphogenesis / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / fibroblast growth factor binding / male meiosis I / monocyte chemotaxis / BH3 domain binding / Protein hydroxylation / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / TOR signaling / positive regulation of GTPase activity / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / iron-sulfur cluster binding / regulation of cell division / Peptide chain elongation / cellular response to ethanol / Selenocysteine synthesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Formation of a pool of free 40S subunits / negative regulation of protein binding / protein serine/threonine kinase inhibitor activity / Eukaryotic Translation Termination / blastocyst development / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of respiratory burst involved in inflammatory response / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / negative regulation of ubiquitin-dependent protein catabolic process / 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 / protein targeting / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity 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: 2.42 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_36180.map.gz | 516.7 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-36180-v30.xml emd-36180.xml | 104.3 KB 104.3 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_36180_fsc.xml | 18.7 KB | 表示 | FSCデータファイル |
| 画像 | emd_36180.png | 78.1 KB | ||
| Filedesc metadata | emd-36180.cif.gz | 21.3 KB | ||
| その他 | emd_36180_additional_1.map.gz emd_36180_half_map_1.map.gz emd_36180_half_map_2.map.gz | 455.4 MB 456.7 MB 456.6 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-36180 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36180 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 8jdlMC ![]() 7y7cC ![]() 7y7dC ![]() 7y7eC ![]() 7y7fC ![]() 7y7gC ![]() 7y7hC ![]() 8jdjC ![]() 8jdkC ![]() 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 ( |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_36180.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_36180_additional_1.map | ||||||||||||
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| 注釈 | before postprocess | ||||||||||||
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| 密度ヒストグラム |
-ハーフマップ: #2
| ファイル | emd_36180_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_36180_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 |
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試料の構成要素
+全体 : The complex of Human 80S Ribosome with mRNA and P- site tRNA
+超分子 #1: The complex of Human 80S Ribosome with mRNA and P- site tRNA
+分子 #1: mRNA
+分子 #2: tRNA (Tyr)
+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: beta-D-galactopyranose
+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 |
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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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| 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 |
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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: 32000 / 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 |
ムービー
コントローラー
万見について




キーワード
Homo sapiens (ヒト)
データ登録者
日本, 3件
引用


















































Z (Sec.)
Y (Row.)
X (Col.)













































解析
FIELD EMISSION GUN


