+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8g1u | ||||||
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タイトル | Structure of the methylosome-Lsm10/11 complex | ||||||
要素 |
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キーワード | TRANSFERASE / Methylation / GENE REGULATION | ||||||
機能・相同性 | 機能・相同性情報 : / snRNP Assembly / mRNA 3'-end processing by stem-loop binding and cleavage / positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation ...: / snRNP Assembly / mRNA 3'-end processing by stem-loop binding and cleavage / positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway / peptidyl-arginine N-methylation / oocyte axis specification / type II protein arginine methyltransferase / protein-arginine omega-N symmetric methyltransferase activity / peptidyl-arginine methylation / Golgi ribbon formation / negative regulation of epithelial cell proliferation involved in prostate gland development / histone H4R3 methyltransferase activity / negative regulation of cell volume / regulation of chromatin organization / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / U7 snRNA binding / U7 snRNP / histone arginine N-methyltransferase activity / histone pre-mRNA 3'end processing complex / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / epithelial cell proliferation involved in prostate gland development / protein-arginine N-methyltransferase activity / methylosome / cell volume homeostasis / pICln-Sm protein complex / methyl-CpG binding / telomerase holoenzyme complex / mRNA cis splicing, via spliceosome / endothelial cell activation / histone H3 methyltransferase activity / positive regulation of mRNA splicing, via spliceosome / chloride transport / RNA Polymerase II Transcription Termination / negative regulation of gene expression via chromosomal CpG island methylation / regulation of mitotic nuclear division / histone methyltransferase complex / Cul4B-RING E3 ubiquitin ligase complex / positive regulation of oligodendrocyte differentiation / histone methyltransferase activity / E-box binding / negative regulation of cell differentiation / ubiquitin-like ligase-substrate adaptor activity / positive regulation of G1/S transition of mitotic cell cycle / ribonucleoprotein complex binding / spliceosomal snRNP assembly / regulation of ERK1 and ERK2 cascade / nuclear receptor coactivator activity / regulation of signal transduction by p53 class mediator / methyltransferase activity / liver regeneration / DNA-templated transcription termination / spliceosomal complex / circadian regulation of gene expression / Regulation of TP53 Activity through Methylation / RMTs methylate histone arginines / protein polyubiquitination / transcription corepressor activity / p53 binding / snRNP Assembly / ubiquitin-dependent protein catabolic process / cytoskeleton / nuclear body / chromatin remodeling / protein heterodimerization activity / positive regulation of cell population proliferation / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / Golgi apparatus / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Mus musculus (ハツカネズミ) | ||||||
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: 2.83 Å | ||||||
データ登録者 | Lin, M. / Paige, A. / Tong, L. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: RNA / 年: 2023 タイトル: In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome. 著者: Xiao-Cui Yang / Anthony Desotell / Min-Han Lin / Andrew S Paige / Agata Malinowska / Yadong Sun / Wei Shen Aik / Michał Dadlez / Liang Tong / Zbigniew Dominski / 要旨: U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 ...U7 snRNP is a multisubunit endonuclease required for 3' end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B, and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50, and pICln known to methylate arginines in the carboxy-terminal regions of the Sm proteins B, D1, and D3 during the spliceosomal Sm ring assembly. Both biochemical and cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the amino-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an amino-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP. | ||||||
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 | 8g1u.cif.gz | 674.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8g1u.ent.gz | 531.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8g1u.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 | 8g1u_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8g1u_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 8g1u_validation.xml.gz | 100.1 KB | 表示 | |
CIF形式データ | 8g1u_validation.cif.gz | 153 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/g1/8g1u ftp://data.pdbj.org/pub/pdb/validation_reports/g1/8g1u | HTTPS FTP |
-関連構造データ
関連構造データ | 29677MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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: 72766.664 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PRMT5, HRMT1L5, IBP72, JBP1, SKB1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) 参照: UniProt: O14744, type II protein arginine methyltransferase #2: タンパク質 | 分子量: 36757.246 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: WDR77, MEP50, WD45, HKMT1069, Nbla10071 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q9BQA1 #3: タンパク質 | 分子量: 26038.957 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Clns1a, Clci, Clcni / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q61189 #4: タンパク質 | 分子量: 39572.793 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: LSM11 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P83369 #5: 化合物 | ChemComp-ADN / 研究の焦点であるリガンドがあるか | Y | |
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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: Methylosome / タイプ: COMPLEX / Entity ID: #1-#4 / 由来: RECOMBINANT |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Trichoplusia ni (イラクサキンウワバ) |
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 | 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 / 最大 デフォーカス(公称値): 1250 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 58.2 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.18.2_3874: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 2.83 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 754047 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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