+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7xw3 | ||||||
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タイトル | Cryo-EM structure of an apo-form of human DICER | ||||||
要素 | Endoribonuclease Dicer | ||||||
キーワード | GENE REGULATION / Dicer / RNaseIII / RNA-binding / micro-RNA processing | ||||||
機能・相同性 | 機能・相同性情報 peripheral nervous system myelin formation / global gene silencing by mRNA cleavage / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / tRNA decay / positive regulation of myelination / apoptotic DNA fragmentation / ribonuclease III ...peripheral nervous system myelin formation / global gene silencing by mRNA cleavage / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / tRNA decay / positive regulation of myelination / apoptotic DNA fragmentation / ribonuclease III / deoxyribonuclease I activity / positive regulation of Schwann cell differentiation / nerve development / RISC-loading complex / miRNA metabolic process / RISC complex assembly / miRNA processing / ribonuclease III activity / pre-miRNA processing / siRNA binding / siRNA processing / Regulation of MITF-M-dependent genes involved in apoptosis / M-decay: degradation of maternal mRNAs by maternally stored factors / RISC complex / MicroRNA (miRNA) biogenesis / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA endonuclease activity / neuron projection morphogenesis / helicase activity / double-stranded RNA binding / protein domain specific binding / negative regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
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: 4.04 Å | ||||||
データ登録者 | Lee, H. / Roh, S.-H. | ||||||
資金援助 | 韓国, 1件
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引用 | ジャーナル: Nature / 年: 2023 タイトル: Structure of the human DICER-pre-miRNA complex in a dicing state. 著者: Young-Yoon Lee / Hansol Lee / Haedong Kim / V Narry Kim / Soung-Hun Roh / 要旨: Dicer has a key role in small RNA biogenesis, processing double-stranded RNAs (dsRNAs). Human DICER (hDICER, also known as DICER1) is specialized for cleaving small hairpin structures such as ...Dicer has a key role in small RNA biogenesis, processing double-stranded RNAs (dsRNAs). Human DICER (hDICER, also known as DICER1) is specialized for cleaving small hairpin structures such as precursor microRNAs (pre-miRNAs) and has limited activity towards long dsRNAs-unlike its homologues in lower eukaryotes and plants, which cleave long dsRNAs. Although the mechanism by which long dsRNAs are cleaved has been well documented, our understanding of pre-miRNA processing is incomplete because structures of hDICER in a catalytic state are lacking. Here we report the cryo-electron microscopy structure of hDICER bound to pre-miRNA in a dicing state and uncover the structural basis of pre-miRNA processing. hDICER undergoes large conformational changes to attain the active state. The helicase domain becomes flexible, which allows the binding of pre-miRNA to the catalytic valley. The double-stranded RNA-binding domain relocates and anchors pre-miRNA in a specific position through both sequence-independent and sequence-specific recognition of the newly identified 'GYM motif'. The DICER-specific PAZ helix is also reoriented to accommodate the RNA. Furthermore, our structure identifies a configuration of the 5' end of pre-miRNA inserted into a basic pocket. In this pocket, a group of arginine residues recognize the 5' terminal base (disfavouring guanine) and terminal monophosphate; this explains the specificity of hDICER and how it determines the cleavage site. We identify cancer-associated mutations in the 5' pocket residues that impair miRNA biogenesis. Our study reveals how hDICER recognizes pre-miRNAs with stringent specificity and enables a mechanistic understanding of hDICER-related diseases. | ||||||
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 | 7xw3.cif.gz | 281.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7xw3.ent.gz | 221.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7xw3.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 | 7xw3_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7xw3_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 7xw3_validation.xml.gz | 58.1 KB | 表示 | |
CIF形式データ | 7xw3_validation.cif.gz | 85.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/xw/7xw3 ftp://data.pdbj.org/pub/pdb/validation_reports/xw/7xw3 | HTTPS FTP |
-関連構造データ
関連構造データ | 33490MC 7xw2C 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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-要素
#1: タンパク質 | 分子量: 218947.328 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: DICER1, DICER, HERNA, KIAA0928 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q9UPY3, ribonuclease III |
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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: 3D ARRAY / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: monomeric form of human DICER / タイプ: COMPLEX / Entity ID: all / 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: Homo sapiens (ヒト) |
緩衝液 | pH: 8 |
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: 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: 288 K / 詳細: blot force 5 and blot for 2 seconds |
-電子顕微鏡撮影
顕微鏡 | モデル: TFS GLACIOS |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 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): 2750 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) |
-解析
CTF補正 | タイプ: NONE |
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3次元再構成 | 解像度: 4.04 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 128635 / 対称性のタイプ: POINT |