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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 | High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | ribosome / rRNA ribomethylome | |||||||||
| 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 / 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 / positive regulation of microtubule polymerization 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: 2.5 Å | |||||||||
データ登録者 | Cheng J / Beckmann R | |||||||||
| 資金援助 | 1件
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引用 | ジャーナル: Cancer Discov / 年: 2023タイトル: A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia. 著者: Fengbiao Zhou / Nesrine Aroua / Yi Liu / Christian Rohde / Jingdong Cheng / Anna-Katharina Wirth / Daria Fijalkowska / Stefanie Göllner / Michelle Lotze / Haiyang Yun / Xiaobing Yu / ...著者: Fengbiao Zhou / Nesrine Aroua / Yi Liu / Christian Rohde / Jingdong Cheng / Anna-Katharina Wirth / Daria Fijalkowska / Stefanie Göllner / Michelle Lotze / Haiyang Yun / Xiaobing Yu / Caroline Pabst / Tim Sauer / Thomas Oellerich / Hubert Serve / Christoph Röllig / Martin Bornhäuser / Christian Thiede / Claudia Baldus / Michaela Frye / Simon Raffel / Jeroen Krijgsveld / Irmela Jeremias / Roland Beckmann / Andreas Trumpp / Carsten Müller-Tidow / ![]() 要旨: The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O- ...The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O-methylation regulate leukemia stem cell (LSC) activity in vivo. A comprehensive analysis of the rRNA 2'-O-methylation landscape of 94 patients with acute myeloid leukemia (AML) revealed dynamic 2'-O-methylation specifically at exterior sites of ribosomes. The rRNA 2'-O-methylation pattern is closely associated with AML development stage and LSC gene expression signature. Forced expression of the 2'-O-methyltransferase fibrillarin (FBL) induced an AML stem cell phenotype and enabled engraftment of non-LSC leukemia cells in NSG mice. Enhanced 2'-O-methylation redirected the ribosome translation program toward amino acid transporter mRNAs enriched in optimal codons and subsequently increased intracellular amino acid levels. Methylation at the single site 18S-guanosine 1447 was instrumental for LSC activity. Collectively, our work demonstrates that dynamic 2'-O-methylation at specific sites on rRNAs shifts translational preferences and controls AML LSC self-renewal. SIGNIFICANCE: We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process ...SIGNIFICANCE: We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process constitutes a novel concept of how cancers reprogram cell fate and function. This article is highlighted in the In This Issue feature, p. 247. | |||||||||
| 履歴 |
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構造の表示
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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_33330.map.gz | 243.6 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-33330-v30.xml emd-33330.xml | 100.3 KB 100.3 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_33330_fsc.xml | 14.7 KB | 表示 | FSCデータファイル |
| 画像 | emd_33330.png | 234.5 KB | ||
| Filedesc metadata | emd-33330.cif.gz | 20.2 KB | ||
| その他 | emd_33330_half_map_1.map.gz emd_33330_half_map_2.map.gz | 225 MB 225 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-33330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33330 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 7xnyMC ![]() 7xnxC 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_33330.map.gz / 形式: CCP4 / 大きさ: 282.6 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: 1.059 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
-ハーフマップ: #1
| ファイル | emd_33330_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: #2
| ファイル | emd_33330_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 : ribosome
+超分子 #1: ribosome
+分子 #1: 28S rRNA
+分子 #2: 5S rRNA
+分子 #3: 5.8S rRNA
+分子 #46: 18S rRNA
+分子 #4: 60S ribosomal protein L8
+分子 #5: 60S ribosomal protein L3
+分子 #6: 60S ribosomal protein L4
+分子 #7: 60S ribosomal protein L5
+分子 #8: 60S ribosomal protein L6
+分子 #9: 60S ribosomal protein L7
+分子 #10: 60S ribosomal protein L7a
+分子 #11: 60S ribosomal protein L9
+分子 #12: Ribosomal protein L10 isoform A
+分子 #13: 60S ribosomal protein L11
+分子 #14: 60S ribosomal protein L13
+分子 #15: 60S ribosomal protein L14
+分子 #16: 60S ribosomal protein L15
+分子 #17: 60S ribosomal protein L13a
+分子 #18: 60S ribosomal protein L17
+分子 #19: 60S ribosomal protein L18
+分子 #20: 60S ribosomal protein L19
+分子 #21: 60S ribosomal protein L18a
+分子 #22: 60S ribosomal protein L21
+分子 #23: 60S ribosomal protein L22
+分子 #24: 60S ribosomal protein L23
+分子 #25: 60S ribosomal protein L24
+分子 #26: 60S ribosomal protein L23a
+分子 #27: 60S ribosomal protein L26
+分子 #28: 60S ribosomal protein L27
+分子 #29: 60S ribosomal protein L27a
+分子 #30: 60S ribosomal protein L29
+分子 #31: 60S ribosomal protein L30
+分子 #32: 60S ribosomal protein L31
+分子 #33: 60S ribosomal protein L32
+分子 #34: 60S ribosomal protein L35a
+分子 #35: 60S ribosomal protein L34
+分子 #36: 60S ribosomal protein L35
+分子 #37: 60S ribosomal protein L36
+分子 #38: 60S ribosomal protein L37
+分子 #39: 60S ribosomal protein L38
+分子 #40: 60S ribosomal protein L39
+分子 #41: Ubiquitin-60S ribosomal protein L40
+分子 #42: 60S ribosomal protein L41
+分子 #43: 60S ribosomal protein L36a
+分子 #44: 60S ribosomal protein L37a
+分子 #45: 60S ribosomal protein L28
+分子 #47: 40S ribosomal protein SA
+分子 #48: 40S ribosomal protein S3a
+分子 #49: 40S ribosomal protein S3
+分子 #50: 40S ribosomal protein S4, X isoform
+分子 #51: 40S ribosomal protein S5
+分子 #52: 40S ribosomal protein S7
+分子 #53: 40S ribosomal protein S8
+分子 #54: 40S ribosomal protein S10
+分子 #55: 40S ribosomal protein S11
+分子 #56: 40S ribosomal protein S15
+分子 #57: 40S ribosomal protein S16
+分子 #58: 40S ribosomal protein S17
+分子 #59: 40S ribosomal protein S18
+分子 #60: 40S ribosomal protein S19
+分子 #61: 40S ribosomal protein S20
+分子 #62: 40S ribosomal protein S21
+分子 #63: 40S ribosomal protein S23
+分子 #64: 40S ribosomal protein S26
+分子 #65: 40S ribosomal protein S28
+分子 #66: 40S ribosomal protein S29
+分子 #67: Receptor of activated protein C kinase 1
+分子 #68: 40S ribosomal protein S2
+分子 #69: 40S ribosomal protein S6
+分子 #70: 40S ribosomal protein S9
+分子 #71: 40S ribosomal protein S12
+分子 #72: 40S ribosomal protein S13
+分子 #73: 40S ribosomal protein S14
+分子 #74: 40S ribosomal protein S15a
+分子 #75: 40S ribosomal protein S24
+分子 #76: 40S ribosomal protein S25
+分子 #77: 40S ribosomal protein S27
+分子 #78: 40S ribosomal protein S30
+分子 #79: Ubiquitin-40S ribosomal protein S27a
+分子 #80: MAGNESIUM ION
+分子 #81: POTASSIUM ION
+分子 #82: ZINC ION
+分子 #83: water
-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 |
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| 凍結 | 凍結剤: ETHANE |
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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 K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 44.0 e/Å2 |
| 電子線 | 加速電圧: 300 kV / 電子線源: TUNGSTEN HAIRPIN |
| 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): 0.8 µm |
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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万見について




キーワード
Homo sapiens (ヒト)
データ登録者
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Z (Sec.)
Y (Row.)
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解析

