+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-11099 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1 | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
キーワード | Ribosome / hibernation | |||||||||
機能・相同性 | 機能・相同性情報 Synthesis of diphthamide-EEF2 / membraneless organelle / ribosome hibernation / translation elongation factor binding / PML body organization / SUMO binding / eukaryotic 80S initiation complex / negative regulation of protein neddylation / : / translation at presynapse ...Synthesis of diphthamide-EEF2 / membraneless organelle / ribosome hibernation / translation elongation factor binding / PML body organization / SUMO binding / eukaryotic 80S initiation complex / negative regulation of protein neddylation / : / translation at presynapse / negative regulation of endoplasmic reticulum unfolded protein response / axial mesoderm development / ribosomal protein import into nucleus / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / 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 / 90S preribosome assembly / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 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 / NF-kappaB complex / middle ear morphogenesis / neural crest cell differentiation / ubiquitin-like protein conjugating enzyme binding / aggresome / regulation of establishment of cell polarity / negative regulation of phagocytosis / A band / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / alpha-beta T cell differentiation / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / optic nerve development / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Uptake and function of diphtheria toxin / response to aldosterone / retinal ganglion cell axon guidance / Translation initiation complex formation / homeostatic process / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / G1 to G0 transition / macrophage chemotaxis / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / lung morphogenesis / iron-sulfur cluster binding / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / positive regulation of activated T cell proliferation / male meiosis I / monocyte chemotaxis / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / regulation of cell division / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / 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 / translational elongation / negative regulation of respiratory burst involved in inflammatory response / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane 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: 3.1 Å | |||||||||
データ登録者 | Wells JN / Buschauer R | |||||||||
引用 | ジャーナル: PLoS Biol / 年: 2020 タイトル: Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. 著者: Jennifer N Wells / Robert Buschauer / Timur Mackens-Kiani / Katharina Best / Hanna Kratzat / Otto Berninghausen / Thomas Becker / Wendy Gilbert / Jingdong Cheng / Roland Beckmann / 要旨: Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with ...Cells adjust to nutrient deprivation by reversible translational shutdown. This is accompanied by maintaining inactive ribosomes in a hibernation state, in which they are bound by proteins with inhibitory and protective functions. In eukaryotes, such a function was attributed to suppressor of target of Myb protein 1 (Stm1; SERPINE1 mRNA-binding protein 1 [SERBP1] in mammals), and recently, late-annotated short open reading frame 2 (Lso2; coiled-coil domain containing short open reading frame 124 [CCDC124] in mammals) was found to be involved in translational recovery after starvation from stationary phase. Here, we present cryo-electron microscopy (cryo-EM) structures of translationally inactive yeast and human ribosomes. We found Lso2/CCDC124 accumulating on idle ribosomes in the nonrotated state, in contrast to Stm1/SERBP1-bound ribosomes, which display a rotated state. Lso2/CCDC124 bridges the decoding sites of the small with the GTPase activating center (GAC) of the large subunit. This position allows accommodation of the duplication of multilocus region 34 protein (Dom34)-dependent ribosome recycling system, which splits Lso2-containing, but not Stm1-containing, ribosomes. We propose a model in which Lso2 facilitates rapid translation reactivation by stabilizing the recycling-competent state of inactive ribosomes. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_11099.map.gz | 144 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-11099-v30.xml emd-11099.xml | 100.8 KB 100.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_11099_fsc.xml | 14.2 KB | 表示 | FSCデータファイル |
画像 | emd_11099.png | 239.6 KB | ||
Filedesc metadata | emd-11099.cif.gz | 20.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-11099 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11099 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_11099_validation.pdf.gz | 285.6 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_11099_full_validation.pdf.gz | 284.7 KB | 表示 | |
XML形式データ | emd_11099_validation.xml.gz | 14 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11099 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11099 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_11099.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: 1.061 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
+全体 : 80S ribosome bound to EBP1, eEF2 and SERBP1
+超分子 #1: 80S ribosome bound to EBP1, eEF2 and SERBP1
+分子 #1: 28S rRNA
+分子 #2: 5S rRNA
+分子 #3: 5.8S rRNA
+分子 #47: 18S rRNA
+分子 #83: tRNA
+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: 60S ribosomal protein L10-like
+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 #46: 60S ribosomal protein L10a
+分子 #48: 40S ribosomal protein SA
+分子 #49: 40S ribosomal protein S3a
+分子 #50: 40S ribosomal protein S3
+分子 #51: 40S ribosomal protein S4, X isoform
+分子 #52: 40S ribosomal protein S5
+分子 #53: 40S ribosomal protein S7
+分子 #54: 40S ribosomal protein S8
+分子 #55: 40S ribosomal protein S10
+分子 #56: 40S ribosomal protein S11
+分子 #57: 40S ribosomal protein S15
+分子 #58: 40S ribosomal protein S16
+分子 #59: 40S ribosomal protein S17
+分子 #60: 40S ribosomal protein S18
+分子 #61: 40S ribosomal protein S19
+分子 #62: 40S ribosomal protein S20
+分子 #63: 40S ribosomal protein S21
+分子 #64: 40S ribosomal protein S23
+分子 #65: 40S ribosomal protein S26
+分子 #66: 40S ribosomal protein S28
+分子 #67: 40S ribosomal protein S29
+分子 #68: Receptor of activated protein C kinase 1
+分子 #69: 40S ribosomal protein S2
+分子 #70: 40S ribosomal protein S6
+分子 #71: 40S ribosomal protein S9
+分子 #72: 40S ribosomal protein S12
+分子 #73: 40S ribosomal protein S13
+分子 #74: 40S ribosomal protein S14
+分子 #75: 40S ribosomal protein S15a
+分子 #76: 40S ribosomal protein S24
+分子 #77: 40S ribosomal protein S25
+分子 #78: 40S ribosomal protein S27
+分子 #79: 40S ribosomal protein S30
+分子 #80: Ubiquitin-40S ribosomal protein S27a
+分子 #81: Proliferation-associated protein 2G4
+分子 #82: Elongation factor 2
+分子 #84: Plasminogen activator inhibitor 1 RNA-binding protein
+分子 #85: MAGNESIUM ION
+分子 #86: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: FEI FALCON III (4k x 4k) 平均電子線量: 28.0 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |