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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 80S consensus ribosome with EBP1 | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Ribosome / In situ | |||||||||
| 機能・相同性 | 機能・相同性情報cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / host-mediated activation of viral genome replication / ribosome hibernation / translation elongation factor binding / PML body organization ...cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / host-mediated activation of viral genome replication / ribosome hibernation / translation elongation factor binding / PML body organization / SUMO binding / 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 / kinase activator activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of ubiquitin-protein transferase activity / 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 / 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 / cortical actin cytoskeleton / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / protein kinase A binding / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / laminin receptor activity / Translation initiation complex formation / homeostatic process / pigmentation / 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 / Protein hydroxylation / negative regulation of translational frameshifting / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / TOR signaling / positive regulation of GTPase activity / iron-sulfur cluster binding / mTORC1-mediated signalling / Peptide chain elongation / regulation of cell division / Selenocysteine synthesis / Formation of a pool of free 40S subunits / cellular response to ethanol / translational elongation / blastocyst development / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of protein binding / protein serine/threonine kinase inhibitor activity / Viral mRNA Translation / ubiquitin ligase inhibitor activity / HSF1 activation / negative regulation of respiratory burst involved in inflammatory 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: 2.67 Å | |||||||||
データ登録者 | Wei Z / Yong X | |||||||||
| 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. | |||||||||
| 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_71435.map.gz | 258.1 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-71435-v30.xml emd-71435.xml | 109.4 KB 109.4 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_71435_fsc.xml | 16.8 KB | 表示 | FSCデータファイル |
| 画像 | emd_71435.png | 90.3 KB | ||
| Filedesc metadata | emd-71435.cif.gz | 21.3 KB | ||
| その他 | emd_71435_half_map_1.map.gz emd_71435_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-71435 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-71435 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9pa7MC ![]() 9p6zC ![]() 9p72C ![]() 9p73C ![]() 9p76C ![]() 9p78C ![]() 9p79C ![]() 9p7aC ![]() 9p7cC ![]() 9p7dC ![]() 9p7eC ![]() 9p7fC ![]() 9p7gC ![]() 9p7hC ![]() 9p7iC ![]() 9p7jC ![]() 9p7kC ![]() 9p7lC ![]() 9p7nC ![]() 9p7oC ![]() 9p7wC ![]() 9p7xC ![]() 9p7yC ![]() 9p8bC ![]() 9p8cC ![]() 9p8hC ![]() 9p8iC ![]() 9p9hC ![]() 9p9iC ![]() 9p9jC ![]() 9p9kC ![]() 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_71435.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_71435_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_71435_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 : In situ human 80S consensus ribosome with EBP1
+超分子 #1: In situ human 80S consensus ribosome with EBP1
+分子 #1: SERPINE1 mRNA-binding protein 1
+分子 #2: Transcription factor BTF3
+分子 #3: Elongation factor 1-alpha 1
+分子 #7: 60S ribosomal protein L8
+分子 #8: Large ribosomal subunit protein uL3
+分子 #9: 60S ribosomal protein L4
+分子 #10: Large ribosomal subunit protein uL18
+分子 #11: Large ribosomal subunit protein eL6
+分子 #12: 60S ribosomal protein L7
+分子 #13: 60S ribosomal protein L7a
+分子 #14: 60S ribosomal protein L9
+分子 #15: Ribosomal protein uL16-like
+分子 #16: 60S ribosomal protein L11
+分子 #17: Large ribosomal subunit protein eL13
+分子 #18: 60S ribosomal protein L14
+分子 #19: 60S ribosomal protein L15
+分子 #20: 60S ribosomal protein L13a
+分子 #21: 60S ribosomal protein L17
+分子 #22: 60S ribosomal protein L18
+分子 #23: 60S ribosomal protein L19
+分子 #24: 60S ribosomal protein L18a
+分子 #25: 60S ribosomal protein L21
+分子 #26: Heparin-binding protein HBp15
+分子 #27: 60S ribosomal protein L23
+分子 #28: Ribosomal protein L24
+分子 #29: 60S ribosomal protein L23a
+分子 #30: 60S ribosomal protein L26
+分子 #31: 60S ribosomal protein L27
+分子 #32: 60S ribosomal protein L27a
+分子 #33: Large ribosomal subunit protein eL29
+分子 #34: 60S ribosomal protein L30
+分子 #35: 60S ribosomal protein L31
+分子 #36: 60S ribosomal protein L32
+分子 #37: 60S ribosomal protein L35a
+分子 #38: 60S ribosomal protein L34
+分子 #39: 60S ribosomal protein L35
+分子 #40: 60S ribosomal protein L36
+分子 #41: 60S ribosomal protein L37
+分子 #42: 60S ribosomal protein L38
+分子 #43: 60S ribosomal protein L39
+分子 #44: Large ribosomal subunit protein eL40
+分子 #45: 60S ribosomal protein L41
+分子 #46: 60S ribosomal protein L36a
+分子 #47: 60S ribosomal protein L37a
+分子 #48: 60S ribosomal protein L28
+分子 #49: 60S acidic ribosomal protein P0
+分子 #50: Large ribosomal subunit protein uL11
+分子 #53: 40S ribosomal protein SA
+分子 #54: 40S ribosomal protein S3a
+分子 #55: 40S ribosomal protein S2
+分子 #56: Small ribosomal subunit protein uS3
+分子 #57: Small ribosomal subunit protein eS4, X isoform
+分子 #58: 40S ribosomal protein S5
+分子 #59: 40S ribosomal protein S6
+分子 #60: Small ribosomal subunit protein eS7
+分子 #61: 40S ribosomal protein S8
+分子 #62: 40S ribosomal protein S9
+分子 #63: 40S ribosomal protein S10
+分子 #64: 40S ribosomal protein S11
+分子 #65: Small ribosomal subunit protein eS12
+分子 #66: 40S ribosomal protein S13
+分子 #67: Small ribosomal subunit protein uS11
+分子 #68: Small ribosomal subunit protein uS19
+分子 #69: Small ribosomal subunit protein uS9
+分子 #70: Small ribosomal subunit protein eS17
+分子 #71: 40S ribosomal protein S18
+分子 #72: 40S ribosomal protein S19
+分子 #73: 40S ribosomal protein S20
+分子 #74: Small ribosomal subunit protein eS21
+分子 #75: 40S ribosomal protein S15a
+分子 #76: 40S ribosomal protein S23
+分子 #77: 40S ribosomal protein S24
+分子 #78: Small ribosomal subunit protein eS25
+分子 #79: 40S ribosomal protein S26
+分子 #80: Small ribosomal subunit protein eS27
+分子 #81: 40S ribosomal protein S28
+分子 #82: 40S ribosomal protein S29
+分子 #83: Small ribosomal subunit protein eS30
+分子 #84: Ubiquitin-40S ribosomal protein S27a
+分子 #85: Receptor of activated protein C kinase 1
+分子 #87: Proliferation-associated protein 2G4
+分子 #4: 28S rRNA
+分子 #5: 5S rRNA
+分子 #6: 5.8S rRNA
+分子 #51: P site tRNA
+分子 #52: 18S rRNA
+分子 #86: A/T site tRNA
+分子 #88: MAGNESIUM ION
+分子 #89: SPERMINE
+分子 #90: SPERMIDINE
+分子 #91: POTASSIUM ION
+分子 #92: ZINC ION
+分子 #93: 1,4-DIAMINOBUTANE
+分子 #94: 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 | 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.)
X (Col.)








































解析
FIELD EMISSION GUN


