+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5mc6 | ||||||
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タイトル | Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae | ||||||
要素 |
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キーワード | RIBOSOME / cryo-EM / RNA / helicase | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / mRNA decay by 3' to 5' exoribonuclease / Ski complex / protein-DNA complex assembly / positive regulation of translational termination / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / mRNA decay by 3' to 5' exoribonuclease / Ski complex / protein-DNA complex assembly / positive regulation of translational termination / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear-transcribed mRNA catabolic process, non-stop decay / positive regulation of translational elongation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / negative regulation of glucose mediated signaling pathway / negative regulation of translational frameshifting / Negative regulators of DDX58/IFIH1 signaling / Protein methylation / positive regulation of translational fidelity / RMTs methylate histone arginines / mTORC1-mediated signalling / Protein hydroxylation / reciprocal meiotic recombination / ribosome-associated ubiquitin-dependent protein catabolic process / GDP-dissociation inhibitor activity / nonfunctional rRNA decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / pre-mRNA 5'-splice site binding / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Ribosomal scanning and start codon recognition / response to cycloheximide / nuclear chromosome / 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 / mRNA catabolic process / 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 / negative regulation of mRNA splicing, via spliceosome / nuclear-transcribed mRNA catabolic process / regulation of amino acid metabolic process / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / G-protein alpha-subunit binding / positive regulation of protein kinase activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / Ub-specific processing proteases / regulation of translational fidelity / protein-RNA complex assembly / positive regulation of translational initiation / translation elongation factor activity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / 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 / ribosome assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / macroautophagy / protein kinase C binding / maintenance of translational fidelity / cytoplasmic stress granule / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / ribosome biogenesis / small ribosomal subunit rRNA binding / ribosome binding / ribosomal large subunit assembly / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic small ribosomal subunit / protein-containing complex assembly / defense response to virus / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / negative regulation of translation / rRNA binding / ribosome 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 | Schmidt, C. / Kowalinski, E. / Shanmuganathan, V. / Defenouillere, Q. / Braunger, K. / Heuer, A. / Pech, M. / Namane, A. / Berninghausen, O. / Fromont-Racine, M. ...Schmidt, C. / Kowalinski, E. / Shanmuganathan, V. / Defenouillere, Q. / Braunger, K. / Heuer, A. / Pech, M. / Namane, A. / Berninghausen, O. / Fromont-Racine, M. / Jacquier, A. / Conti, E. / Becker, T. / Beckmann, R. | ||||||
引用 | ジャーナル: Science / 年: 2016 タイトル: The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex. 著者: Christian Schmidt / Eva Kowalinski / Vivekanandan Shanmuganathan / Quentin Defenouillère / Katharina Braunger / André Heuer / Markus Pech / Abdelkader Namane / Otto Berninghausen / ...著者: Christian Schmidt / Eva Kowalinski / Vivekanandan Shanmuganathan / Quentin Defenouillère / Katharina Braunger / André Heuer / Markus Pech / Abdelkader Namane / Otto Berninghausen / Micheline Fromont-Racine / Alain Jacquier / Elena Conti / Thomas Becker / Roland Beckmann / 要旨: Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski ...Ski2-Ski3-Ski8 (Ski) is a helicase complex functioning with the RNA-degrading exosome to mediate the 3'-5' messenger RNA (mRNA) decay in turnover and quality-control pathways. We report that the Ski complex directly associates with 80S ribosomes presenting a short mRNA 3' overhang. We determined the structure of an endogenous ribosome-Ski complex using cryo-electron microscopy (EM) with a local resolution of the Ski complex ranging from 4 angstroms (Å) in the core to about 10 Å for intrinsically flexible regions. Ribosome binding displaces the autoinhibitory domain of the Ski2 helicase, positioning it in an open conformation near the ribosomal mRNA entry tunnel. We observe that the mRNA 3' overhang is threaded directly from the small ribosomal subunit to the helicase channel of Ski2, primed for ongoing exosome-mediated 3'-5' degradation. | ||||||
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 | 5mc6.cif.gz | 5.6 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5mc6.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 5mc6.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 | 5mc6_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 5mc6_full_validation.pdf.gz | 1.9 MB | 表示 | |
XML形式データ | 5mc6_validation.xml.gz | 389.8 KB | 表示 | |
CIF形式データ | 5mc6_validation.cif.gz | 679.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/mc/5mc6 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/5mc6 | 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 , 7種, 7分子 2lmnBQBRBS
#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 (strain ATCC 204508 / S288c) (パン酵母) 参照: REF: 831416132 |
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#35: RNA鎖 | 分子量: 10494.894 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) |
#36: RNA鎖 | 分子量: 24378.408 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) |
#37: RNA鎖 | 分子量: 24815.684 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) |
#83: RNA鎖 | 分子量: 1097493.875 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: REF: 831416132 |
#84: RNA鎖 | 分子量: 38951.105 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: 1039024045 |
#85: RNA鎖 | 分子量: 50682.922 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: 1102645687 |
+40S ribosomal protein ... , 31種, 31分子 ABCDEFGHIJKLMPQRSTUVWXYZabcdefg
-タンパク質 , 8種, 9分子 NOhijkAOAZBT
#15: 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) 参照: UniProt: P05759 | ||||||
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#16: 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 | ||||||
#38: タンパク質 | 分子量: 146259.094 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: P35207, RNA helicase | ||||||
#39: タンパク質 | 分子量: 163922.141 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: P17883 | ||||||
#40: タンパク質 | 分子量: 44283.527 Da / 分子数: 2 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) 参照: UniProt: Q02793 #55: タンパク質 | | 分子量: 14583.077 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: P0CH08 #66: タンパク質 | | 分子量: 17889.996 Da / 分子数: 1 / 由来タイプ: 天然 詳細: Due to resolution, this protein was only built as a poly-ala model. The actual uL1 sequence can be obtained from Uniprot-ID P0CX43. We had the same situation with a previous deposition of our group (PDB-ID 5GAK). 由来: (天然) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) #86: タンパク質 | | 分子量: 17222.406 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: P23301 |
+60S ribosomal protein ... , 40種, 40分子 AAABACADAEAFAGAHAIAJAKALAMANAPAQARASATAUAVAWAXAYBABBBCBDBEBF...
-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: Native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae タイプ: RIBOSOME / Entity ID: #1-#87 / 由来: NATURAL | |||||||||||||||||||||||||||||||||||
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分子量 | 値: 3.6 MDa / 実験値: NO | |||||||||||||||||||||||||||||||||||
由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) | |||||||||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | |||||||||||||||||||||||||||||||||||
緩衝液成分 |
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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/PALLADIUM / グリッドのタイプ: Quantifoil R3/3 | |||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 278 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 / Cs: 2.7 mm / アライメント法: COMA FREE |
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: 2.8 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 撮影したグリッド数: 2 |
画像スキャン | 利用したフレーム数/画像: 1-10 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 31503 / 対称性のタイプ: POINT |