+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23500 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | 80S ribosome from mouse bound to eEF2 (Class II) | |||||||||
マップデータ | unsharpened map | |||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 Peptide chain elongation / Synthesis of diphthamide-EEF2 / TNFR1-mediated ceramide production / 5.8S rRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Protein hydroxylation / positive regulation of amide metabolic process / translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / TNFR1-mediated ceramide production / 5.8S rRNA binding / Formation of the ternary complex, and subsequently, the 43S complex / Protein hydroxylation / positive regulation of amide metabolic process / translation at postsynapse / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / ER Quality Control Compartment (ERQC) / Regulation of PTEN localization / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of expression of SLITs and ROBOs / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Alpha-protein kinase 1 signaling pathway / Stabilization of p53 / Formation of a pool of free 40S subunits / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Pexophagy / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / SRP-dependent cotranslational protein targeting to membrane / NRIF signals cell death from the nucleus / Translesion synthesis by POLI / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of BACH1 activity / Recognition of DNA damage by PCNA-containing replication complex / p75NTR recruits signalling complexes / HDR through Homologous Recombination (HRR) / Interferon alpha/beta signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Negative regulation of MAPK pathway / membraneless organelle / Spry regulation of FGF signaling / Regulation of innate immune responses to cytosolic DNA / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / Dual Incision in GG-NER / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / TNFR1-induced NF-kappa-B signaling pathway / Downregulation of ERBB2 signaling / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / Dual incision in TC-NER / Inactivation of CSF3 (G-CSF) signaling / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Oncogene Induced Senescence / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Translation initiation complex formation / Ribosomal scanning and start codon recognition / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TCF dependent signaling in response to WNT / Metalloprotease DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / EGFR downregulation / SCF(Skp2)-mediated degradation of p27/p21 / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) / Mouse (ネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
データ登録者 | Loerch S / Smith PR / Kunder N / Stanowick AD / Lou T-F / Campbell ZT | |||||||||
資金援助 | 米国, 2件
| |||||||||
引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance. 著者: Patrick R Smith / Sarah Loerch / Nikesh Kunder / Alexander D Stanowick / Tzu-Fang Lou / Zachary T Campbell / 要旨: Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible ...Processing bodies (p-bodies) are a prototypical phase-separated RNA-containing granule. Their abundance is highly dynamic and has been linked to translation. Yet, the molecular mechanisms responsible for coordinate control of the two processes are unclear. Here, we uncover key roles for eEF2 kinase (eEF2K) in the control of ribosome availability and p-body abundance. eEF2K acts on a sole known substrate, eEF2, to inhibit translation. We find that the eEF2K agonist nelfinavir abolishes p-bodies in sensory neurons and impairs translation. To probe the latter, we used cryo-electron microscopy. Nelfinavir stabilizes vacant 80S ribosomes. They contain SERBP1 in place of mRNA and eEF2 in the acceptor site. Phosphorylated eEF2 associates with inactive ribosomes that resist splitting in vitro. Collectively, the data suggest that eEF2K defines a population of inactive ribosomes resistant to recycling and protected from degradation. Thus, eEF2K activity is central to both p-body abundance and ribosome availability in sensory neurons. | |||||||||
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_23500.map.gz | 1.6 GB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-23500-v30.xml emd-23500.xml | 100.6 KB 100.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_23500.png | 230.4 KB | ||
その他 | emd_23500_half_map_1.map.gz emd_23500_half_map_2.map.gz | 98.3 MB 98.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23500 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23500 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23500_validation.pdf.gz | 786 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_23500_full_validation.pdf.gz | 785.5 KB | 表示 | |
XML形式データ | emd_23500_validation.xml.gz | 25.9 KB | 表示 | |
CIF形式データ | emd_23500_validation.cif.gz | 30.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23500 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23500 | 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_23500.map.gz / 形式: CCP4 / 大きさ: 1.7 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | unsharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.06 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
-ハーフマップ: odd
ファイル | emd_23500_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | odd | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: even
ファイル | emd_23500_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | even | ||||||||||||
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : 80S ribosome from mous ebound to eEF2
+超分子 #1: 80S ribosome from mous ebound to eEF2
+分子 #1: 60S ribosomal protein L7
+分子 #2: 60S ribosomal protein L7a
+分子 #3: 60S ribosomal protein L9
+分子 #4: 60S ribosomal protein L10-like
+分子 #5: 60S ribosomal protein L11
+分子 #6: 60S ribosomal protein L13
+分子 #7: 60S ribosomal protein L14
+分子 #8: 60S ribosomal protein L15
+分子 #12: 60S ribosomal protein L8
+分子 #13: 60S ribosomal protein L3
+分子 #14: 60S ribosomal protein L4
+分子 #15: 60S ribosomal protein L5
+分子 #16: 60S ribosomal protein L6
+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 #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 S11
+分子 #52: 40S ribosomal protein S17
+分子 #53: 40S ribosomal protein SA
+分子 #54: 40S ribosomal protein S5
+分子 #55: 40S ribosomal protein S10
+分子 #56: 40S ribosomal protein S15
+分子 #57: 40S ribosomal protein S16
+分子 #58: 40S ribosomal protein S18
+分子 #59: 40S ribosomal protein S19
+分子 #60: 40S ribosomal protein S20
+分子 #61: 40S ribosomal protein S21
+分子 #62: 40S ribosomal protein S23
+分子 #63: 40S ribosomal protein S26
+分子 #64: 40S ribosomal protein S28
+分子 #65: 40S ribosomal protein S29
+分子 #66: Receptor of activated protein C kinase 1
+分子 #67: 40S ribosomal protein S2
+分子 #68: 40S ribosomal protein S6
+分子 #69: 40S ribosomal protein S9
+分子 #70: 40S ribosomal protein S12
+分子 #71: 40S ribosomal protein S13
+分子 #72: 40S ribosomal protein S14
+分子 #73: 40S ribosomal protein S15a
+分子 #74: 40S ribosomal protein S24
+分子 #75: 40S ribosomal protein S25
+分子 #76: 40S ribosomal protein S27-like
+分子 #77: 40S ribosomal protein S30
+分子 #78: Ubiquitin-40S ribosomal protein S27a
+分子 #79: Elongation factor 2
+分子 #80: 60S acidic ribosomal protein P0
+分子 #81: 60S ribosomal protein L12
+分子 #82: Isoform 3 of Plasminogen activator inhibitor 1 RNA-binding protein
+分子 #83: 40S ribosomal protein S7
+分子 #84: 40S ribosomal protein S8
+分子 #85: 60S ribosomal protein L10a
+分子 #9: 28S rRNA
+分子 #10: 5S rRNA
+分子 #11: 5.8S rRNA
+分子 #46: 28S rRNA
+分子 #47: tRNA
+分子 #86: ZINC ION
+分子 #87: MAGNESIUM ION
+分子 #88: GUANOSINE-5'-DIPHOSPHATE
+分子 #89: water
-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: 7.5 |
---|---|
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV / 詳細: 3 second blotting, force 3. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
特殊光学系 | エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 1.0 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 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
---|---|
得られたモデル | PDB-7ls1: |