+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12535 | |||||||||
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タイトル | Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA | |||||||||
マップデータ | map colliding ribosome | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process ...maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / pre-mRNA 5'-splice site binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / response to cycloheximide / mRNA destabilization / Major pathway of rRNA processing in the nucleolus and cytosol / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / positive regulation of protein kinase activity / protein-RNA complex assembly / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribosomal small subunit export from nucleus / translational termination / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / maturation of LSU-rRNA / cellular response to amino acid starvation / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / transcription coactivator activity / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288c (パン酵母) / Saccharomyces cerevisiae S288C (パン酵母) / Baker's yeast (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.36 Å | |||||||||
データ登録者 | Pochopien AA / Beckert B / Wilson DN | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2021 タイトル: Structure of Gcn1 bound to stalled and colliding 80S ribosomes. 著者: Agnieszka A Pochopien / Bertrand Beckert / Sergo Kasvandik / Otto Berninghausen / Roland Beckmann / Tanel Tenson / Daniel N Wilson / 要旨: The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for ...The Gcn pathway is conserved in all eukaryotes, including mammals such as humans, where it is a crucial part of the integrated stress response (ISR). Gcn1 serves as an essential effector protein for the kinase Gcn2, which in turn is activated by stalled ribosomes, leading to phosphorylation of eIF2 and a subsequent global repression of translation. The fine-tuning of this adaptive response is performed by the Rbg2/Gir2 complex, a negative regulator of Gcn2. Despite the wealth of available biochemical data, information on structures of Gcn proteins on the ribosome has remained elusive. Here we present a cryo-electron microscopy structure of the yeast Gcn1 protein in complex with stalled and colliding 80S ribosomes. Gcn1 interacts with both 80S ribosomes within the disome, such that the Gcn1 HEAT repeats span from the P-stalk region on the colliding ribosome to the P-stalk and the A-site region of the lead ribosome. The lead ribosome is stalled in a nonrotated state with peptidyl-tRNA in the A-site, uncharged tRNA in the P-site, eIF5A in the E-site, and Rbg2/Gir2 in the A-site factor binding region. By contrast, the colliding ribosome adopts a rotated state with peptidyl-tRNA in a hybrid A/P-site, uncharged-tRNA in the P/E-site, and Mbf1 bound adjacent to the mRNA entry channel on the 40S subunit. Collectively, our findings reveal the interaction mode of the Gcn2-activating protein Gcn1 with colliding ribosomes and provide insight into the regulation of Gcn2 activation. The binding of Gcn1 to a disome has important implications not only for the Gcn2-activated ISR, but also for the general ribosome-associated quality control pathways. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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_12535.map.gz | 697.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12535-v30.xml emd-12535.xml | 97.9 KB 97.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12535_fsc.xml | 25 KB | 表示 | FSCデータファイル |
画像 | emd_12535.png | 174.2 KB | ||
その他 | emd_12535_additional_1.map.gz emd_12535_additional_2.map.gz emd_12535_additional_3.map.gz emd_12535_half_map_1.map.gz emd_12535_half_map_2.map.gz | 251.2 MB 11.5 MB 48.9 MB 1 GB 1 GB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12535 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12535 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12535_validation.pdf.gz | 367.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12535_full_validation.pdf.gz | 366.8 KB | 表示 | |
XML形式データ | emd_12535_validation.xml.gz | 29.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12535 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12535 | HTTPS FTP |
-関連構造データ
-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 |
-マップ
ファイル | ダウンロード / ファイル: emd_12535.map.gz / 形式: CCP4 / 大きさ: 1.3 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | map colliding ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: map colliding ribosome relion final run
ファイル | emd_12535_additional_1.map | ||||||||||||
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注釈 | map colliding ribosome relion final run | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focus refinement 40S only and postprocess
ファイル | emd_12535_additional_2.map | ||||||||||||
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注釈 | focus refinement 40S only and postprocess | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: map colliding ribosome postprocess
ファイル | emd_12535_additional_3.map | ||||||||||||
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注釈 | map colliding ribosome postprocess | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map colliding ribosome
ファイル | emd_12535_half_map_1.map | ||||||||||||
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注釈 | Half map colliding ribosome | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map colliding ribosome
ファイル | emd_12535_half_map_2.map | ||||||||||||
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注釈 | Half map colliding ribosome | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Structure of the yeast Gcn1-bound coilliding stalled 80S ribosome...
+超分子 #1: Structure of the yeast Gcn1-bound coilliding stalled 80S ribosome...
+分子 #1: TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete ...
+分子 #36: mRNA (32-MER)
+分子 #37: tRNA (75-MER)
+分子 #38: tRNA (77-MER)
+分子 #39: 25S rRNA (3184-MER)
+分子 #40: 5S rRNA (121-MER)
+分子 #41: 5.8S rRNA (158-MER)
+分子 #2: 40S ribosomal protein S3
+分子 #3: 40S ribosomal protein S5
+分子 #4: 40S ribosomal protein S10-A
+分子 #5: 40S ribosomal protein S12
+分子 #6: 40S ribosomal protein S15
+分子 #7: 40S ribosomal protein S16-A
+分子 #8: 40S ribosomal protein S17-B
+分子 #9: 40S ribosomal protein S18-A
+分子 #10: 40S ribosomal protein S19-A
+分子 #11: 40S ribosomal protein S20
+分子 #12: 40S ribosomal protein S25-A
+分子 #13: 40S ribosomal protein S28-A
+分子 #14: 40S ribosomal protein S29-A
+分子 #15: Ubiquitin-40S ribosomal protein S31
+分子 #16: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #17: 40S ribosomal protein S0-A
+分子 #18: 40S ribosomal protein S1-A
+分子 #19: 40S ribosomal protein S2
+分子 #20: 40S ribosomal protein S4-A
+分子 #21: 40S ribosomal protein S6-A
+分子 #22: 40S ribosomal protein S7-A
+分子 #23: 40S ribosomal protein S8-A
+分子 #24: 40S ribosomal protein S9-A
+分子 #25: 40S ribosomal protein S11-A
+分子 #26: 40S ribosomal protein S13
+分子 #27: 40S ribosomal protein S14-B
+分子 #28: 40S ribosomal protein S21-A
+分子 #29: 40S ribosomal protein S22-A
+分子 #30: 40S ribosomal protein S23-A
+分子 #31: 40S ribosomal protein S24-A
+分子 #32: 40S ribosomal protein S26-B
+分子 #33: 40S ribosomal protein S27-A
+分子 #34: 40S ribosomal protein S30-A
+分子 #35: Multiprotein-bridging factor 1
+分子 #42: 60S ribosomal protein L2-A
+分子 #43: 60S ribosomal protein L3
+分子 #44: 60S ribosomal protein L4-A
+分子 #45: 60S ribosomal protein L5
+分子 #46: 60S ribosomal protein L6-B
+分子 #47: 60S ribosomal protein L7-A
+分子 #48: 60S ribosomal protein L8-A
+分子 #49: 60S ribosomal protein L9-A
+分子 #50: 60S ribosomal protein L10
+分子 #51: 60S ribosomal protein L11-B
+分子 #52: 60S ribosomal protein L13-A
+分子 #53: 60S ribosomal protein L14-A
+分子 #54: 60S ribosomal protein L15-A
+分子 #55: 60S ribosomal protein L16-A
+分子 #56: 60S ribosomal protein L17-A
+分子 #57: 60S ribosomal protein L18-A
+分子 #58: 60S ribosomal protein L19-A
+分子 #59: 60S ribosomal protein L20-A
+分子 #60: 60S ribosomal protein L21-A
+分子 #61: 60S ribosomal protein L22-A
+分子 #62: 60S ribosomal protein L23-A
+分子 #63: 60S ribosomal protein L24-A
+分子 #64: 60S ribosomal protein L25
+分子 #65: 60S ribosomal protein L26-A
+分子 #66: 60S ribosomal protein L27-A
+分子 #67: 60S ribosomal protein L28
+分子 #68: 60S ribosomal protein L29
+分子 #69: 60S ribosomal protein L30
+分子 #70: 60S ribosomal protein L31-A
+分子 #71: 60S ribosomal protein L32
+分子 #72: 60S ribosomal protein L33-A
+分子 #73: 60S ribosomal protein L34-A
+分子 #74: 60S ribosomal protein L35-A
+分子 #75: 60S ribosomal protein L36-A
+分子 #76: 60S ribosomal protein L37-A
+分子 #77: 60S ribosomal protein L38
+分子 #78: 60S ribosomal protein L39
+分子 #79: Ubiquitin-60S ribosomal protein L40
+分子 #80: 60S ribosomal protein L41-B
+分子 #81: 60S ribosomal protein L42-A
+分子 #82: 60S ribosomal protein L43-A
-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 |
-試料調製
緩衝液 | pH: 7.5 |
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グリッド | モデル: Quantifoil R3/3 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 300.0 nm |
凍結 | 凍結剤: ETHANE-PROPANE |
-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: FEI FALCON II (4k x 4k) 平均電子線量: 2.5 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: SPOT SCAN / 撮影モード: BRIGHT FIELD |
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 |
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得られたモデル | PDB-7nrd: |