+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6oig | ||||||||||||
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タイトル | Subunit joining exposes nascent pre-40S rRNA for processing and quality control | ||||||||||||
要素 |
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キーワード | RIBOSOME / 80S-like complex / 60S | ||||||||||||
機能・相同性 | 機能・相同性情報 pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / 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 ...pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / 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 / preribosome, large subunit precursor / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of LSU-rRNA / ribosomal large subunit biogenesis / macroautophagy / maintenance of translational fidelity / ribosomal large subunit assembly / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / RNA 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: 3.8 Å | ||||||||||||
データ登録者 | Rai, J. / Parker, M.D. / Ghalei, H. / Johnson, M.C. / Karbstein, K. / Stroupe, M.E. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: RNA / 年: 2021 タイトル: An open interface in the pre-80S ribosome coordinated by ribosome assembly factors Tsr1 and Dim1 enables temporal regulation of Fap7. 著者: Jay Rai / Melissa D Parker / Haina Huang / Stefan Choy / Homa Ghalei / Matthew C Johnson / Katrin Karbstein / M Elizabeth Stroupe / 要旨: During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly ...During their maturation, nascent 40S subunits enter a translation-like quality control cycle, where they are joined by mature 60S subunits to form 80S-like ribosomes. While these assembly intermediates are essential for maturation and quality control, how they form, and how their structure promotes quality control, remains unknown. To address these questions, we determined the structure of an 80S-like ribosome assembly intermediate to an overall resolution of 3.4 Å. The structure, validated by biochemical data, resolves a large body of previously paradoxical data and illustrates how assembly and translation factors cooperate to promote the formation of an interface that lacks many mature subunit contacts but is stabilized by the universally conserved methyltransferase Dim1. We also show how Tsr1 enables this interface by blocking the canonical binding of eIF5B to 40S subunits, while maintaining its binding to 60S. The structure also shows how this interface leads to unfolding of the platform, which allows for temporal regulation of the ATPase Fap7, thus linking 40S maturation to quality control during ribosome assembly. | ||||||||||||
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 | 6oig.cif.gz | 2.9 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6oig.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6oig.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 | 6oig_validation.pdf.gz | 1.1 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6oig_full_validation.pdf.gz | 1.4 MB | 表示 | |
XML形式データ | 6oig_validation.xml.gz | 228.5 KB | 表示 | |
CIF形式データ | 6oig_validation.cif.gz | 390.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oig ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oig | 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
+60S ribosomal protein ... , 41種, 41分子 zABCDEFGHIJsLMNOPQRSTUVWXYZabc...
-タンパク質 , 2種, 2分子 mq
#40: タンパク質 | 分子量: 6032.321 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 遺伝子: RPL40A, UBI1, YIL148W / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CH08 |
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#43: タンパク質 | 分子量: 23585.346 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 遺伝子: RPP0, L10E, RPA0, RPL10E, RPLA0, YLR340W, L8300.8 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05317 |
-RNA鎖 , 3種, 3分子 587
#44: RNA鎖 | 分子量: 1096842.375 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 発現宿主: Saccharomyces cerevisiae (パン酵母) |
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#45: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1267176496 |
#46: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1039024045 |
-タンパク質・ペプチド , 2種, 2分子 xy
#47: タンパク質・ペプチド | 分子量: 4017.944 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 発現宿主: Saccharomyces cerevisiae (パン酵母) |
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#48: タンパク質・ペプチド | 分子量: 3932.839 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 発現宿主: Saccharomyces cerevisiae (パン酵母) |
-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: 60S subunit of 80S-like ribosome / タイプ: RIBOSOME / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
由来(組換発現) | 生物種: Saccharomyces cerevisiae (パン酵母) |
緩衝液 | pH: 6.8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: unspecified |
急速凍結 | 凍結剤: ETHANE |
-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: 25 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: DIRECT ELECTRON DE-64 (8k x 8k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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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: 83558 / 対称性のタイプ: POINT |