+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6y7c | ||||||
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タイトル | Early cytoplasmic yeast pre-40S particle (purified with Tsr1 as bait) | ||||||
要素 |
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キーワード | RIBOSOME / yeast pre-ribosomal particle - small ribosomal subunit | ||||||
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 regulators of DDX58/IFIH1 signaling / endocytic recycling / rRNA primary transcript binding / RMTs methylate histone arginines / positive regulation of translational fidelity ...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 regulators of DDX58/IFIH1 signaling / endocytic recycling / rRNA primary transcript binding / RMTs methylate histone arginines / positive regulation of translational fidelity / Protein methylation / mTORC1-mediated signalling / Protein hydroxylation / U3 snoRNA binding / response to osmotic stress / poly(A)+ mRNA export from nucleus / 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 / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / snoRNA binding / 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 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 90S preribosome / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ub-specific processing proteases / regulation of translational fidelity / ribonucleoprotein complex binding / ribosomal subunit export from nucleus / 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) / 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 / maintenance of translational fidelity / cytoplasmic stress granule / rRNA processing / ribosomal small subunit biogenesis / late endosome / unfolded protein binding / protein transport / small ribosomal subunit rRNA binding / ribosome biogenesis / late endosome membrane / ribosomal small subunit assembly / cellular response to oxidative stress / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / non-specific serine/threonine protein kinase / protein kinase activity / rRNA binding / ribosome / structural constituent of ribosome / translation / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / mRNA binding / GTP binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm 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: 3.8 Å | ||||||
データ登録者 | Shayan, R. / Plassart, L. / Plisson-Chastang, C. | ||||||
資金援助 | フランス, 1件
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引用 | ジャーナル: Molecules / 年: 2020 タイトル: Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy. 著者: Ramtin Shayan / Dana Rinaldi / Natacha Larburu / Laura Plassart / Stéphanie Balor / David Bouyssié / Simon Lebaron / Julien Marcoux / Pierre-Emmanuel Gleizes / Célia Plisson-Chastang / 要旨: Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past ...Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis has been drastically improved by the "resolution revolution" of cryo-electron microscopy (cryo-EM). However, if very early maturation events have been well characterized for both yeast ribosomal subunits, little is known regarding the final maturation steps occurring to the small (40S) ribosomal subunit. To try to bridge this gap, we have used proteomics together with cryo-EM and single particle analysis to characterize yeast pre-40S particles containing the ribosome biogenesis factor Tsr1. Our analyses lead us to refine the timing of the early pre-40S particle maturation steps. Furthermore, we suggest that after an early and structurally stable stage, the beak and platform domains of pre-40S particles enter a "vibrating" or "wriggling" stage, that might be involved in the final maturation of 18S rRNA as well as the fitting of late ribosomal proteins into their mature position. | ||||||
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 | 6y7c.cif.gz | 1.8 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6y7c.ent.gz | 1.4 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6y7c.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 | 6y7c_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6y7c_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 6y7c_validation.xml.gz | 169.9 KB | 表示 | |
CIF形式データ | 6y7c_validation.cif.gz | 283.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/y7/6y7c ftp://data.pdbj.org/pub/pdb/validation_reports/y7/6y7c | 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
-RNA鎖 , 1種, 1分子 2
#1: RNA鎖 | 分子量: 558895.688 Da / 分子数: 1 / 由来タイプ: 天然 詳細: Ribose 2'-O methylation on adenosins A100, A420,A436, A796 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) |
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+40S ribosomal protein ... , 28種, 28分子 ABCEFGHIJLMNOPQRSTUVWXYZbcde
-タンパク質 , 5種, 5分子 hijlt
#30: 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 |
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#31: 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 |
#32: 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 |
#33: 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 |
#34: 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 |
-詳細
研究の焦点であるリガンドがあるか | N |
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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: early cytoplasmic yeast pre-40S particle (purified using Tsr1 as bait) タイプ: RIBOSOME / Entity ID: all / 由来: NATURAL |
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分子量 | 値: 1.8 MDa / 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 |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/1 |
急速凍結 | 装置: LEICA EM GP / 凍結剤: ETHANE / 湿度: 95 % / 凍結前の試料温度: 292 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 |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 29.4 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.12_2829: / 分類: 精密化 | ||||||||||||||||||||||||||||||||
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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: 3.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 19564 / アルゴリズム: EXACT BACK PROJECTION / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER | ||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6FAI Accession code: 6FAI / Source name: PDB / タイプ: experimental model | ||||||||||||||||||||||||||||||||
拘束条件 |
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