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基本情報
登録情報 | データベース: PDB / ID: 7yyn | |||||||||
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タイトル | Mammalian Dicer in the dicing state with pre-miR-15a substrate | |||||||||
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![]() | RNA BINDING PROTEIN / endoribonuclease / dsRNA / complex / gene silencing / post-transcriptional / catalytic complex / cytoplasm | |||||||||
機能・相同性 | ![]() regulation of muscle cell apoptotic process / myoblast differentiation involved in skeletal muscle regeneration / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / ganglion development / hair follicle cell proliferation / zygote asymmetric cell division / regulation of oligodendrocyte differentiation / cardiac neural crest cell development involved in outflow tract morphogenesis / positive regulation of endothelial cell-matrix adhesion via fibronectin ...regulation of muscle cell apoptotic process / myoblast differentiation involved in skeletal muscle regeneration / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / ganglion development / hair follicle cell proliferation / zygote asymmetric cell division / regulation of oligodendrocyte differentiation / cardiac neural crest cell development involved in outflow tract morphogenesis / positive regulation of endothelial cell-matrix adhesion via fibronectin / olfactory bulb interneuron differentiation / regulation of enamel mineralization / positive regulation of establishment of endothelial barrier / positive regulation of hepatic stellate cell proliferation / trophectodermal cell proliferation / regulation of miRNA metabolic process / regulation of odontogenesis of dentin-containing tooth / spermatogonial cell division / regulation of RNA metabolic process / peripheral nervous system myelin formation / regulation of epithelial cell differentiation / regulation of regulatory T cell differentiation / regulation of Notch signaling pathway / spinal cord motor neuron differentiation / global gene silencing by mRNA cleavage / epidermis morphogenesis / negative regulation of Schwann cell proliferation / reproductive structure development / ribonuclease III / positive regulation of myelination / apoptotic DNA fragmentation / inner ear receptor cell development / nerve development / meiotic spindle organization / positive regulation of Schwann cell differentiation / RISC-loading complex / deoxyribonuclease I activity / RISC complex assembly / intestinal epithelial cell development / ribonuclease III activity / regulatory ncRNA-mediated post-transcriptional gene silencing / pericentric heterochromatin formation / miRNA processing / regulation of stem cell differentiation / pre-miRNA processing / regulation of viral genome replication / siRNA processing / digestive tract development / mRNA stabilization / embryonic hindlimb morphogenesis / cartilage development / cardiac muscle cell development / RISC complex / embryonic limb morphogenesis / miRNA binding / positive regulation of vascular endothelial cell proliferation / regulation of myelination / regulation of neuron differentiation / negative regulation of glial cell proliferation / hair follicle morphogenesis / stem cell population maintenance / branching morphogenesis of an epithelial tube / positive regulation of miRNA metabolic process / endoplasmic reticulum-Golgi intermediate compartment / regulation of neurogenesis / hair follicle development / positive regulation of collagen biosynthetic process / postsynaptic density, intracellular component / spindle assembly / RNA processing / spleen development / positive regulation of endothelial cell migration / helicase activity / neuron projection morphogenesis / post-embryonic development / regulation of protein phosphorylation / lung development / multicellular organism growth / cerebral cortex development / rRNA processing / gene expression / growth cone / regulation of inflammatory response / regulation of gene expression / angiogenesis / defense response to virus / cell population proliferation / regulation of cell cycle / axon / glutamatergic synapse / dendrite / positive regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / ATP binding / nucleus / metal ion binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
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: 6.21 Å | |||||||||
![]() | Zanova, M. / Zapletal, D. / Kubicek, K. / Stefl, R. / Pinkas, M. / Novacek, J. | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural and functional basis of mammalian microRNA biogenesis by Dicer. 著者: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / Michaela ...著者: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / Michaela Prochazkova / Jan Prochazka / Matyas Pinkas / Jiri Novacek / Diego F Joseph / Radislav Sedlacek / Carrie Bernecky / Dónal O'Carroll / Richard Stefl / Petr Svoboda / ![]() ![]() ![]() ![]() ![]() 要旨: MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is ...MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer's DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer•-miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways. | |||||||||
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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 | ![]() | 312.9 KB | 表示 | ![]() |
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PDB形式 | ![]() | 234 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 | ![]() | 1.1 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.1 MB | 表示 | |
XML形式データ | ![]() | 41.4 KB | 表示 | |
CIF形式データ | ![]() | 61.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 14384MC ![]() 7yymC ![]() 7yz4C ![]() 7zpiC ![]() 7zpjC ![]() 7zpkC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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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: RNA鎖 | 分子量: 19017.279 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) ![]() ![]() |
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#2: タンパク質 | 分子量: 200040.938 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 発現宿主: ![]() 参照: UniProt: Q8R418, ribonuclease III |
-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 |
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分子量 | 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 8 / 詳細: The buffer was always fresh in RNAse-free manner | ||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.2 mg/ml / 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: 277.15 K / 詳細: Described in STAR methods |
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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 / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 1000 nm |
撮影 | 電子線照射量: 55 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 9956 |
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解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 230362 | |||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 6.21 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 84697 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 36 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 451.4 / プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Correlation coefficient 詳細: Initial model for mouse oocyte Dicer was calculated using AlphaFold 2.0. Initial rigid body fitting was done using Chimera. Further refinement was done using ISOLDE with distance restrains |