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基本情報
登録情報 | データベース: PDB / ID: 7nrc | |||||||||
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タイトル | Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A | |||||||||
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![]() | RIBOSOME / Disome / GCN1 / Translation / GAAC / ISR / Rbg2 / Gir2 | |||||||||
機能・相同性 | ![]() positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / positive regulation of cellular response to amino acid starvation / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / positive regulation of cellular response to amino acid starvation / 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 / positive regulation of translational initiation / translation elongation factor activity / 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 / translation initiation factor 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 / 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 / GTP binding / perinuclear region of cytoplasm / mitochondrion 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
![]() | Pochopien, A.A. / Beckert, B. / Wilson, D.N. | |||||||||
資金援助 | ![]()
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![]() | ![]() 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. | |||||||||
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 4.6 MB | 表示 | ![]() |
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アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
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集合体
登録構造単位 | ![]()
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要素
-RNA鎖 , 7種, 7分子 S2SlSmSnLALBLC
#1: RNA鎖 | 分子量: 579761.938 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: GenBank: 831416132 |
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#2: RNA鎖 | 分子量: 1923.237 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
#36: RNA鎖 | 分子量: 24378.408 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
#37: RNA鎖 | 分子量: 24222.500 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
#40: RNA鎖 | 分子量: 1096842.375 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: GenBank: 831416132 |
#41: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
#42: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
+40S ribosomal protein ... , 32種, 32分子 SPSQSESRSASSSBSTSUSVSWSCSXSDSYSZSFSGSHSISJSaSbScSdSKSeSfSMSgSNSL
-タンパク質 , 5種, 5分子 SOSoLsLtA
#34: タンパク質 | 分子量: 34151.484 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: UniProt: P38011 |
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#38: タンパク質 | 分子量: 40536.207 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: UniProt: P53295 |
#84: タンパク質 | 分子量: 16889.045 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 参照: UniProt: P23301 |
#85: タンパク質 | 分子量: 17889.996 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
#86: タンパク質 | 分子量: 98125.180 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
-タンパク質・ペプチド , 1種, 1分子 Sp
#39: タンパク質・ペプチド | 分子量: 4103.049 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) ![]() ![]() |
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+60S ribosomal protein ... , 41種, 41分子 LDLELFLGLHLILJLKLLLMLNLOLPLQLRLSLTLULVLWLXLYLZLaLbLcLdLeLfLg...
-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 | 名称: Structure of the yeast Gcn1-bound leading stalled 80S ribosome with bound Rbg2, Gir2, A- and P-tRNA and eIF5A タイプ: RIBOSOME / Entity ID: all / 由来: NATURAL |
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分子量 | 実験値: YES |
由来(天然) | 生物種: ![]() ![]() |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE-PROPANE |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 2.5 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
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解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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対称性 | 点対称性: C1 (非対称) |
3次元再構成 | 解像度: 3.9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 30016 / 対称性のタイプ: POINT |