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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7s7c | |||||||||
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タイトル | Human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) | |||||||||
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![]() | RNA BINDING PROTEIN/RNA / Helicase / ATPase / RNA / Exosome / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
機能・相同性 | ![]() snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / RNA catabolic process / regulation of alternative mRNA splicing, via spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / meiotic cell cycle / RNA processing ...snRNA catabolic process / TRAMP complex / snRNA binding / mRNA 3'-end processing / RNA catabolic process / regulation of alternative mRNA splicing, via spliceosome / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / meiotic cell cycle / RNA processing / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA splicing, via spliceosome / rRNA processing / RNA helicase activity / single-stranded RNA binding / nuclear body / RNA helicase / nuclear speck / DNA damage response / nucleolus / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus 類似検索 - 分子機能 | |||||||||
生物種 | ![]() synthetic construct (人工物) | |||||||||
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: 3.62 Å | |||||||||
![]() | Puno, M.R. / Lima, C.D. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural basis for RNA surveillance by the human nuclear exosome targeting (NEXT) complex. 著者: M Rhyan Puno / Christopher D Lima / ![]() 要旨: RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined ...RNA quality control relies on co-factors and adaptors to identify and prepare substrates for degradation by ribonucleases such as the 3' to 5' ribonucleolytic RNA exosome. Here, we determined cryogenic electron microscopy structures of human nuclear exosome targeting (NEXT) complexes bound to RNA that reveal mechanistic insights to substrate recognition and early steps that precede RNA handover to the exosome. The structures illuminate ZCCHC8 as a scaffold, mediating homodimerization while embracing the MTR4 helicase and flexibly anchoring RBM7 to the helicase core. All three subunits collaborate to bind the RNA, with RBM7 and ZCCHC8 surveying sequences upstream of the 3' end to facilitate RNA capture by MTR4. ZCCHC8 obscures MTR4 surfaces important for RNA binding and extrusion as well as MPP6-dependent recruitment and docking onto the RNA exosome core, interactions that contribute to RNA surveillance by coordinating RNA capture, translocation, and extrusion from the helicase to the exosome for decay. | |||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 351.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 258.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 779.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 799 KB | 表示 | |
XML形式データ | ![]() | 48.5 KB | 表示 | |
CIF形式データ | ![]() | 73.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 118224.961 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 69259.805 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #3: タンパク質 | | 分子量: 9462.986 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #4: RNA鎖 | 分子量: 9017.486 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) #5: 化合物 | ChemComp-ZN / | 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 |
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試料調製
構成要素 | 名称: human Nuclear Exosome Targeting (NEXT) complex bound to RNA (substrate 2) タイプ: COMPLEX / Entity ID: #1-#4 / 由来: RECOMBINANT |
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由来(天然) | 生物種: ![]() |
由来(組換発現) | 生物種: ![]() ![]() |
緩衝液 | pH: 8 |
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 / 湿度: 100 % / 凍結前の試料温度: 295 K / 詳細: 30 s wait time, blot for 2.5 s before plunging |
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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: ![]() | ||||||||||||||||||
電子レンズ | モード: BRIGHT FIELD | ||||||||||||||||||
撮影 |
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解析
EMソフトウェア |
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画像処理 | 詳細: 3 datasets collected using Gatan K2 Summit and Gatan K3 image detectors were used for the reconstructions. | |||||||||||||||
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||
3次元再構成 | 解像度: 3.62 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 252638 詳細: A total of 252,638 gave rise to an overall map at 3.62 Angstrom resolution (FSC 0.143 cut off). A composite reconstruction (deposited main map) was generated by combining the overall map with ...詳細: A total of 252,638 gave rise to an overall map at 3.62 Angstrom resolution (FSC 0.143 cut off). A composite reconstruction (deposited main map) was generated by combining the overall map with focused refinement maps of MTR4 core (3.5 Angstrom FSC=0.143), MTR4 core-ZCCHC8 PSP-RBM7-RNA (3.42 Angstrom, FSC=0.143), RBM7-RNA (3.94 Angstrom, FSC=0.143), MTR4-ZCCHC8 HD/KID (3.62 Angstrom, FSC=0.143), and MTR4 KOW-ZCCHC8 HD/KID (3.34 Angstrom, FSC=0.143) regions. 対称性のタイプ: POINT |