+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6fai | ||||||
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タイトル | Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit | ||||||
要素 |
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キーワード | RIBOSOME / pre-40S ribosme / cryo-EM / ribosome assembly / ribosomes / ribosome biogenesis | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of RNA import into nucleus / Ragulator complex / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / endocytic recycling / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding ...positive regulation of RNA import into nucleus / Ragulator complex / ATP export / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / endocytic recycling / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / 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 / U3 snoRNA binding / response to osmotic stress / 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 / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / snoRNA binding / 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) / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of cellular amino acid metabolic process / proteasome assembly / 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 / regulation of translational fidelity / Ub-specific processing proteases / ribosomal subunit export from nucleus / translation regulator activity / ribonucleoprotein complex binding / ribosomal small subunit export from nucleus / 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 / rescue of stalled ribosome / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / unfolded protein binding / protein transport / late endosome / ribosome biogenesis / ribosome binding / late endosome membrane / ribosomal small subunit biogenesis / ribosomal small subunit assembly / cellular response to oxidative stress / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / non-specific serine/threonine protein kinase / negative regulation of translation / ribosome / protein kinase activity / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / mRNA binding / nucleolus / GTP binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | Saccharomyces cerevisiae (パン酵母) | ||||||
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: 3.4 Å | ||||||
データ登録者 | Scaiola, A. / Pena, C. / Weisser, M. / Boehringer, D. / Leibundgut, M. / Klingauf-Nerurkar, P. / Gerhardy, S. / Panse, V.G. / Ban, N. | ||||||
引用 | ジャーナル: EMBO J / 年: 2018 タイトル: Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit. 著者: Alain Scaiola / Cohue Peña / Melanie Weisser / Daniel Böhringer / Marc Leibundgut / Purnima Klingauf-Nerurkar / Stefan Gerhardy / Vikram Govind Panse / Nenad Ban / 要旨: Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron ...Final maturation of eukaryotic ribosomes occurs in the cytoplasm and requires the sequential removal of associated assembly factors and processing of the immature 20S pre-RNA Using cryo-electron microscopy (cryo-EM), we have determined the structure of a yeast cytoplasmic pre-40S particle in complex with Enp1, Ltv1, Rio2, Tsr1, and Pno1 assembly factors poised to initiate final maturation. The structure reveals that the pre-rRNA adopts a highly distorted conformation of its 3' major and 3' minor domains stabilized by the binding of the assembly factors. This observation is consistent with a mechanism that involves concerted release of the assembly factors orchestrated by the folding of the rRNA in the head of the pre-40S subunit during the final stages of maturation. Our results provide a structural framework for the coordination of the final maturation events that drive a pre-40S particle toward the mature form capable of engaging in translation. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6fai.cif.gz | 2.1 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6fai.ent.gz | 1.7 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6fai.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6fai_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6fai_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 6fai_validation.xml.gz | 158.6 KB | 表示 | |
CIF形式データ | 6fai_validation.cif.gz | 278.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/fa/6fai ftp://data.pdbj.org/pub/pdb/validation_reports/fa/6fai | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
+40S ribosomal protein ... , 29種, 29分子 bcdeABCDEFGHIJLMNOPQRSTUVWXYZ
-タンパク質 , 6種, 6分子 ghijkl
#5: タンパク質 | 分子量: 34841.219 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: UniProt: P38011 |
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#6: タンパク質 | 分子量: 30380.623 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: UniProt: Q99216 |
#7: タンパク質 | 分子量: 55207.422 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: UniProt: P38333 |
#8: タンパク質 | 分子量: 53463.254 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: UniProt: P34078 |
#9: タンパク質 | 分子量: 90876.539 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: UniProt: Q07381 |
#10: タンパク質 | 分子量: 49192.852 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: UniProt: P40160, non-specific serine/threonine protein kinase |
-RNA鎖 , 1種, 1分子 2
#11: RNA鎖 | 分子量: 579761.938 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: GenBank: 874346701 |
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-非ポリマー , 2種, 48分子
#37: 化合物 | #38: 化合物 | ChemComp-MG / |
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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 |
-試料調製
構成要素 | 名称: Cytoplasmic pre-40S ribosomal subunit / タイプ: RIBOSOME / Entity ID: #1-#36 / 由来: NATURAL |
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分子量 | 単位: MEGADALTONS / 実験値: NO |
由来(天然) | 生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE-PROPANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-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: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 40 e/Å2 / 検出モード: INTEGRATING フィルム・検出器のモデル: FEI FALCON III (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 165168 / 対称性のタイプ: POINT |