+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7s7b | |||||||||
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タイトル | Human Nuclear exosome targeting (NEXT) complex homodimer bound to RNA (substrate 1) | |||||||||
要素 |
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キーワード | RNA BINDING PROTEIN/RNA / Helicase / ATPase / RNA / Exosome / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
機能・相同性 | 機能・相同性情報 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 / RNA processing / pre-mRNA intronic binding ...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 / RNA processing / pre-mRNA intronic binding / 14-3-3 protein binding / catalytic step 2 spliceosome / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / mRNA Splicing - Major Pathway / meiotic cell cycle / 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 | Homo sapiens (ヒト) 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: 4.06 Å | |||||||||
データ登録者 | Puno, M.R. / Lima, C.D. | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Cell / 年: 2022 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: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7s7b.cif.gz | 510.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7s7b.ent.gz | 402.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7s7b.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 | 7s7b_validation.pdf.gz | 742.2 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7s7b_full_validation.pdf.gz | 771.7 KB | 表示 | |
XML形式データ | 7s7b_validation.xml.gz | 72.8 KB | 表示 | |
CIF形式データ | 7s7b_validation.cif.gz | 111.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/s7/7s7b ftp://data.pdbj.org/pub/pdb/validation_reports/s7/7s7b | 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
#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) Homo sapiens (ヒト) / 遺伝子: MTREX, DOB1, KIAA0052, MTR4, SKIV2L2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P42285, RNA helicase #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) Homo sapiens (ヒト) / 遺伝子: ZCCHC8 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q6NZY4 #3: タンパク質 | 分子量: 9462.986 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: RBM7 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q9Y580 #4: RNA鎖 | 分子量: 14605.818 Da / 分子数: 2 / 由来タイプ: 合成 詳細: The actual RNA sequence is: ACAUGAGGAUCACCCAUGUAAUCUCUUUCAAAAAA(2PU)ACAAAAAAAA. (2PU) is represented by "N" (any nucleotide. This residue is missing in the coordinates and the chemical is an ...詳細: The actual RNA sequence is: ACAUGAGGAUCACCCAUGUAAUCUCUUUCAAAAAA(2PU)ACAAAAAAAA. (2PU) is represented by "N" (any nucleotide. This residue is missing in the coordinates and the chemical is an internal 2' pyrene modified uridine 由来: (合成) synthetic construct (人工物) #5: 化合物 | 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: human Nuclear Exosome Targeting (NEXT)-RNA substrate 1 complex タイプ: COMPLEX / Entity ID: #1-#4 / 由来: RECOMBINANT |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 8 詳細: 20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630 |
試料 | 濃度: 8 mg/ml / 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: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: UltrAuFoil R1.2/1.3 |
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: 295 K / 詳細: 30 s wait time, blot for 2.5 s before plunging |
-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: 67.6 e/Å2 / 検出モード: SUPER-RESOLUTION フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア | 名称: RELION / カテゴリ: 3次元再構成 |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3次元再構成 | 解像度: 4.06 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 618412 詳細: A total of 618,412 particles were used for the consensus reconstruction with an overall resolution of 4.06 Angstrom (FSC 0.143 cut off). Focused 3D classification and local refinement were ...詳細: A total of 618,412 particles were used for the consensus reconstruction with an overall resolution of 4.06 Angstrom (FSC 0.143 cut off). Focused 3D classification and local refinement were performed in several regions of the complex. A composite map was generated using focused reconstructions of ZCCHC8 HD/KID-MTR4 KOW (3.26 Angstrom, FSC = 0.143; 117,561 particles), protomer A MTR4 (3.42 Angstrom, FSC = 0.143; 225,213 particles), protomer B MTR4 (3.54 Angstrom, FSC = 0.143; 236,602 particles), protomer A MTR4 core-ZCCHC8 PSP-RBM7 RRM (4.06 Angstrom, FSC = 0.143; 44,800 particles), and protomer B MTR4 core-ZCCHC8 PSP-RBM7 RRM (4.4 Angstrom, FSC = 0.143 37,088 particles). 対称性のタイプ: POINT |