+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6eml | ||||||
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タイトル | Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae | ||||||
要素 |
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キーワード | RIBOSOME / biogenesis / small subunit / 40S | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of RNA import into nucleus / 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) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / Negative regulators of DDX58/IFIH1 signaling / rRNA primary transcript binding / positive regulation of translational fidelity / Protein methylation / RMTs methylate histone arginines / mTORC1-mediated signalling ...positive regulation of RNA import into nucleus / 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) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / 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 / U3 snoRNA 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 / poly(A)+ mRNA export from nucleus / preribosome, small subunit precursor / 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 / 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 / proteasome assembly / 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 / 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) / 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 / modification-dependent protein catabolic process / cytoplasmic stress granule / rRNA processing / protein tag activity / unfolded protein binding / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytoplasmic translation / rRNA binding / non-specific serine/threonine protein kinase / ribosome / protein kinase activity / protein ubiquitination / structural constituent of ribosome / translation / protein serine kinase activity / protein serine/threonine kinase activity / GTPase activity / mRNA binding / ubiquitin protein ligase binding / nucleolus / GTP binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / 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 (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: 3.6 Å | ||||||
データ登録者 | Heuer, A. / Thomson, E. / Schmidt, C. / Berninghausen, O. / Becker, T. / Hurt, E. / Beckmann, R. | ||||||
引用 | ジャーナル: Elife / 年: 2017 タイトル: Cryo-EM structure of a late pre-40S ribosomal subunit from . 著者: André Heuer / Emma Thomson / Christian Schmidt / Otto Berninghausen / Thomas Becker / Ed Hurt / Roland Beckmann / 要旨: Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the ...Mechanistic understanding of eukaryotic ribosome formation requires a detailed structural knowledge of the numerous assembly intermediates, generated along a complex pathway. Here, we present the structure of a late pre-40S particle at 3.6 Å resolution, revealing in molecular detail how assembly factors regulate the timely folding of pre-18S rRNA. The structure shows that, rather than sterically blocking 40S translational active sites, the associated assembly factors Tsr1, Enp1, Rio2 and Pno1 collectively preclude their final maturation, thereby preventing untimely tRNA and mRNA binding and error prone translation. Moreover, the structure explains how Pno1 coordinates the 3'end cleavage of the 18S rRNA by Nob1 and how the late factor's removal in the cytoplasm ensures the structural integrity of the maturing 40S subunit. | ||||||
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 | 6eml.cif.gz | 1.9 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6eml.ent.gz | 1.5 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6eml.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 | 6eml_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6eml_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 6eml_validation.xml.gz | 159.8 KB | 表示 | |
CIF形式データ | 6eml_validation.cif.gz | 267.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/em/6eml ftp://data.pdbj.org/pub/pdb/validation_reports/em/6eml | 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: 579761.938 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288c (パン酵母) 参照: REF: 831416132 |
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+40S ribosomal protein ... , 26種, 26分子 DBCEFHIKLPQRSTUVWXYZabcdfg
-タンパク質 , 5種, 5分子 Ntpre
#11: タンパク質 | 分子量: 17254.227 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) 株: ATCC 204508 / S288c / 参照: UniProt: P05759 |
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#28: 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) 株: ATCC 204508 / S288c / 参照: UniProt: Q07381 |
#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) 株: ATCC 204508 / S288c / 参照: UniProt: Q99216 |
#31: 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) 株: ATCC 204508 / S288c 参照: UniProt: P40160, non-specific serine/threonine protein kinase |
#32: 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) 株: ATCC 204508 / S288c / 参照: UniProt: P38333 |
-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: late pre-40S ribosomal subunit / タイプ: RIBOSOME / Entity ID: all / 由来: NATURAL |
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分子量 | 値: 1.4 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: 7.5 |
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 |
-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: 2.4 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
EMソフトウェア | 名称: EM-Tools / カテゴリ: 画像取得 |
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CTF補正 | タイプ: NONE |
3次元再構成 | 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 84100 / 対称性のタイプ: POINT |