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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 | In situ human A-P state 80S ribosome | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | In situ / Ribosome | |||||||||
| 機能・相同性 | 機能・相同性情報negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / response to insecticide / eukaryotic 80S initiation complex / regulation of translation involved in cellular response to UV / negative regulation of formation of translation preinitiation complex / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus ...negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / response to insecticide / eukaryotic 80S initiation complex / regulation of translation involved in cellular response to UV / negative regulation of formation of translation preinitiation complex / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / positive regulation of ubiquitin-protein transferase 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 / TNFR1-mediated ceramide production / GAIT complex / negative regulation of RNA splicing / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / oxidized purine DNA binding / cytoplasmic translational initiation / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / regulation of establishment of cell polarity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / laminin receptor activity / homeostatic process / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / 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 / negative regulation of translational frameshifting / TOR signaling / Protein hydroxylation / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / mTORC1-mediated signalling / positive regulation of GTPase activity / Peptide chain elongation / regulation of cell division / Selenocysteine synthesis / cellular response to ethanol / Formation of a pool of free 40S subunits / blastocyst development / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Eukaryotic Translation Termination / protein serine/threonine kinase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of protein binding / Viral mRNA Translation / ubiquitin ligase inhibitor activity / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / positive regulation of microtubule polymerization / regulation of translational fidelity / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) 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: 2.93 Å | |||||||||
データ登録者 | Zheng W / Xiong Y | |||||||||
| 資金援助 | 1件
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引用 | ジャーナル: Nat Commun / 年: 2025タイトル: Visualizing the translation landscape in human cells at high resolution. 著者: Wei Zheng / Yuekang Zhang / Jimin Wang / Shuhui Wang / Pengxin Chai / Elizabeth J Bailey / Chenghao Zhu / Wangbiao Guo / Swapnil C Devarkar / Shenping Wu / Jianfeng Lin / Kai Zhang / Jun Liu ...著者: Wei Zheng / Yuekang Zhang / Jimin Wang / Shuhui Wang / Pengxin Chai / Elizabeth J Bailey / Chenghao Zhu / Wangbiao Guo / Swapnil C Devarkar / Shenping Wu / Jianfeng Lin / Kai Zhang / Jun Liu / Ivan B Lomakin / Yong Xiong / ![]() 要旨: Comprehensive in situ structures of macromolecules can transform our understanding of biology and advance human health. Here, we map protein synthesis inside human cells in detail by combining ...Comprehensive in situ structures of macromolecules can transform our understanding of biology and advance human health. Here, we map protein synthesis inside human cells in detail by combining automated cryo-focused ion beam (FIB) milling and in situ single-particle cryo electron microscopy (cryo-EM). With this in situ cryo-EM approach, we resolved a 2.2 Å consensus structure of the human 80S ribosome and unveiled 23 functional states, nearly all better than 3 Å resolution. Compared to in vitro studies, we observed variations in ribosome structures, distinct environments of ion and polyamine binding, and associated proteins such as EDF1 and NACβ that are typically not enriched with purified ribosomes. We also detected additional peptide-related density features on the ribosome and visualized ribosome-ribosome interactions in helical polysomes. Finally, high-resolution structures from cells treated with homoharringtonine and cycloheximide revealed a distinct translational landscape and a spermidine that interacts with cycloheximide at the E site, one of the numerous polyamines that also bind native ribosomes. These results underscore the value of high-resolution in situ studies in the native environment. | |||||||||
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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_71355.map.gz | 257.9 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-71355-v30.xml emd-71355.xml | 103.4 KB 103.4 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_71355_fsc.xml | 16.8 KB | 表示 | FSCデータファイル |
| 画像 | emd_71355.png | 12.9 KB | ||
| Filedesc metadata | emd-71355.cif.gz | 19.8 KB | ||
| その他 | emd_71355_half_map_1.map.gz emd_71355_half_map_2.map.gz | 475.6 MB 475.6 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-71355 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71355 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9p7wMC ![]() 9p6zC ![]() 9p72C ![]() 9p73C ![]() 9p76C ![]() 9p78C ![]() 9p79C ![]() 9p7aC ![]() 9p7cC ![]() 9p7dC ![]() 9p7eC ![]() 9p7fC ![]() 9p7gC ![]() 9p7hC ![]() 9p7iC ![]() 9p7jC ![]() 9p7kC ![]() 9p7lC ![]() 9p7nC ![]() 9p7oC ![]() 9p7xC ![]() 9p7yC ![]() 9p8bC ![]() 9p8cC ![]() 9p8hC ![]() 9p8iC ![]() 9p9hC ![]() 9p9iC ![]() 9p9jC ![]() 9p9kC ![]() 9pa7C ![]() 9pbeC ![]() 9pkgC 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_71355.map.gz / 形式: CCP4 / 大きさ: 512 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: 1.068 Å | ||||||||||||||||||||||||||||||||||||
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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_71355_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_71355_half_map_2.map | ||||||||||||
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| 投影像・断面図 |
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試料の構成要素
+全体 : In situ human A-P state 80S ribosome
+超分子 #1: In situ human A-P state 80S ribosome
+分子 #1: 40S ribosomal protein SA
+分子 #2: 40S ribosomal protein S3a
+分子 #3: 40S ribosomal protein S2
+分子 #4: Small ribosomal subunit protein eS4, X isoform
+分子 #5: 40S ribosomal protein S6
+分子 #6: Small ribosomal subunit protein eS7
+分子 #7: 40S ribosomal protein S8
+分子 #8: 40S ribosomal protein S9
+分子 #9: 40S ribosomal protein S11
+分子 #10: 40S ribosomal protein S13
+分子 #11: Small ribosomal subunit protein uS11
+分子 #12: Small ribosomal subunit protein eS21
+分子 #13: 40S ribosomal protein S15a
+分子 #14: 40S ribosomal protein S23
+分子 #15: 40S ribosomal protein S24
+分子 #16: 40S ribosomal protein S26
+分子 #17: Small ribosomal subunit protein eS27
+分子 #18: Small ribosomal subunit protein eS30
+分子 #20: 60S ribosomal protein L19
+分子 #21: Ribosomal protein L24
+分子 #22: Small ribosomal subunit protein eS17
+分子 #23: Small ribosomal subunit protein uS3
+分子 #24: 40S ribosomal protein S5
+分子 #25: 40S ribosomal protein S10
+分子 #26: Small ribosomal subunit protein eS12
+分子 #27: Small ribosomal subunit protein uS19
+分子 #28: Small ribosomal subunit protein uS9
+分子 #29: 40S ribosomal protein S18
+分子 #30: 40S ribosomal protein S19
+分子 #31: 40S ribosomal protein S20
+分子 #32: Small ribosomal subunit protein eS25
+分子 #33: 40S ribosomal protein S28
+分子 #34: 40S ribosomal protein S29
+分子 #35: Ubiquitin-40S ribosomal protein S27a
+分子 #36: Receptor of activated protein C kinase 1
+分子 #39: Transcription factor BTF3
+分子 #43: 60S ribosomal protein L8
+分子 #44: Large ribosomal subunit protein uL3
+分子 #45: 60S ribosomal protein L4
+分子 #46: Large ribosomal subunit protein uL18
+分子 #47: Large ribosomal subunit protein eL6
+分子 #48: 60S ribosomal protein L7
+分子 #49: 60S ribosomal protein L7a
+分子 #50: 60S ribosomal protein L9
+分子 #51: Ribosomal protein uL16-like
+分子 #52: 60S ribosomal protein L11
+分子 #53: Large ribosomal subunit protein eL13
+分子 #54: 60S ribosomal protein L14
+分子 #55: 60S ribosomal protein L15
+分子 #56: 60S ribosomal protein L13a
+分子 #57: 60S ribosomal protein L17
+分子 #58: 60S ribosomal protein L18
+分子 #59: 60S ribosomal protein L18a
+分子 #60: 60S ribosomal protein L21
+分子 #61: Heparin-binding protein HBp15
+分子 #62: 60S ribosomal protein L23
+分子 #63: 60S ribosomal protein L23a
+分子 #64: 60S ribosomal protein L26
+分子 #65: 60S ribosomal protein L27
+分子 #66: 60S ribosomal protein L27a
+分子 #67: Large ribosomal subunit protein eL29
+分子 #68: 60S ribosomal protein L30
+分子 #69: 60S ribosomal protein L31
+分子 #70: 60S ribosomal protein L32
+分子 #71: 60S ribosomal protein L35a
+分子 #72: 60S ribosomal protein L34
+分子 #73: 60S ribosomal protein L35
+分子 #74: 60S ribosomal protein L36
+分子 #75: 60S ribosomal protein L37
+分子 #76: 60S ribosomal protein L38
+分子 #77: 60S ribosomal protein L39
+分子 #78: Large ribosomal subunit protein eL40
+分子 #79: 60S ribosomal protein L41
+分子 #80: 60S ribosomal protein L36a
+分子 #81: 60S ribosomal protein L37a
+分子 #82: 60S ribosomal protein L28
+分子 #83: 60S acidic ribosomal protein P0
+分子 #84: Large ribosomal subunit protein uL11
+分子 #19: 18S rRNA [Homo sapiens]
+分子 #37: A site tRNA
+分子 #38: P site tRNA
+分子 #40: 28S rRNA
+分子 #41: 5S rRNA
+分子 #42: 5.8S rRNA
+分子 #85: MAGNESIUM ION
+分子 #86: ZINC ION
+分子 #87: SPERMINE
+分子 #88: SPERMIDINE
-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 | cell |
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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 TECNAI F30 |
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| 撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 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): 1.2 µm |
| 実験機器 | ![]() モデル: Tecnai F30 / 画像提供: FEI Company |
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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
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Z (Sec.)
Y (Row.)
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解析
FIELD EMISSION GUN


