+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 7zpj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Mammalian Dicer in the "pre-dicing state" with pre-miR-15a substrate and TARBP2 subunit | |||||||||
![]() |
| |||||||||
![]() | RNA BINDING PROTEIN / endoribonuclease / dsRNA / complex / gene silencing / post-transcriptional / catalytic complex / cytoplasm / RISC-loading complex / TARBP2 RNA BINDING PROTEIN | |||||||||
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 / regulation of siRNA processing / regulation of miRNA processing / ganglion development / hair follicle cell proliferation / zygote asymmetric cell division / regulation of oligodendrocyte differentiation ...regulation of muscle cell apoptotic process / myoblast differentiation involved in skeletal muscle regeneration / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / regulation of siRNA processing / regulation of miRNA processing / 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 / regulation of viral transcription / 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 / regulation of regulatory ncRNA processing / peripheral nervous system myelin formation / negative regulation of defense response to virus by host / regulation of epithelial cell differentiation / pre-miRNA binding / 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 / skeletal muscle tissue regeneration / 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 / siRNA binding / pre-miRNA processing / regulation of viral genome replication / siRNA processing / neural precursor cell proliferation / 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 / positive regulation of muscle cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / spermatid development / regulation of neurogenesis / hair follicle development / single fertilization / positive regulation of collagen biosynthetic process / postsynaptic density, intracellular component / spindle assembly / positive regulation of viral genome replication / RNA processing / spleen development / positive regulation of endothelial cell migration / helicase activity / neuron projection morphogenesis / post-embryonic development / positive regulation of translation / regulation of protein phosphorylation / lung development / multicellular organism growth / cerebral cortex development / rRNA processing / double-stranded RNA binding / gene expression / growth cone / regulation of inflammatory response / regulation of gene expression 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: 3.81 Å | |||||||||
![]() | Zanova, M. / Zapletal, D. / Kubicek, K. / Stefl, R. / Pinkas, M. / Novacek, J. | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() 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. | |||||||||
履歴 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 525.4 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 411.5 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 | ![]() | 1000.1 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 1006.6 KB | 表示 | |
XML形式データ | ![]() | 49.4 KB | 表示 | |
CIF形式データ | ![]() | 73.4 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 | ![]() 14855MC ![]() 7yymC ![]() 7yynC ![]() 7yz4C ![]() 7zpiC ![]() 7zpkC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
---|---|
類似構造データ | 類似検索 - 機能・相同性 ![]() |
-
リンク
-
集合体
登録構造単位 | ![]()
|
---|---|
1 |
|
-
要素
#1: タンパク質 | 分子量: 226925.656 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
---|---|
#2: RNA鎖 | 分子量: 19017.279 Da / 分子数: 1 / 由来タイプ: 合成 / 詳細: from Mus musculus / 由来: (合成) ![]() ![]() |
#3: タンパク質 | 分子量: 39991.059 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: P97473 |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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 |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
由来(天然) |
| ||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||
緩衝液 | pH: 8 詳細: The buffer was always prepared fresh in RNAse-free manner. | ||||||||||||||||||||||||
緩衝液成分 |
| ||||||||||||||||||||||||
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 |
-
電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
---|---|
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): 800 nm |
撮影 | 電子線照射量: 60.198 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 実像数: 48253 |
-
解析
ソフトウェア | 名称: PHENIX / バージョン: 1.19.2_4158: / 分類: 精密化 | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EMソフトウェア |
| |||||||||||||||||||||||||||||||||||||||||||||
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: 2219694 | |||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.81 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 437518 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 189.2 / プロトコル: FLEXIBLE FIT / 空間: REAL Target criteria: Ramachandran Plot, Rotamer Analysis, Density Fit Analysis, Correlation coefficient 詳細: We used our previous deposition 7YYM as an initial model source. TARBP2 initial coordinates were predicted by AlphaFold. Initial local fitting was done using Chimera and then Coot's Real ...詳細: We used our previous deposition 7YYM as an initial model source. TARBP2 initial coordinates were predicted by AlphaFold. Initial local fitting was done using Chimera and then Coot's Real Space Refine Zone. PHENIX Real-space refinement was used for flexible fitting. ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide chain and distance restraints for polyribonucleotides. | |||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1 / Accession code: 7YYM / Initial refinement model-ID: 1 / PDB-ID: 7YYM / Source name: PDB / タイプ: experimental model
| |||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|