+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14854 | |||||||||
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タイトル | Mammalian Dicer in the "dicing state" with pre-miR-15a substrate | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | endoribonuclease / dsRNA / complex / gene silencing / post-transcriptional / catalytic complex / cytoplasm / RNA BINDING PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 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 / regulation of RNA metabolic process / 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 / peripheral nervous system myelin formation / regulation of epithelial cell differentiation / regulation of regulatory T cell differentiation / global gene silencing by mRNA cleavage / spinal cord motor neuron differentiation / regulation of Notch signaling pathway / 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 / deoxyribonuclease I activity / nerve development / meiotic spindle organization / positive regulation of Schwann cell differentiation / RISC-loading complex / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / intestinal epithelial cell development / miRNA processing / pre-miRNA processing / pericentric heterochromatin formation / regulation of stem cell differentiation / siRNA processing / regulation of viral genome replication / digestive tract development / RISC complex / mRNA stabilization / embryonic hindlimb morphogenesis / cartilage development / cardiac muscle cell development / embryonic limb morphogenesis / miRNA binding / positive regulation of miRNA metabolic process / positive regulation of vascular endothelial cell proliferation / regulation of neuron differentiation / regulation of myelination / negative regulation of glial cell proliferation / hair follicle morphogenesis / stem cell population maintenance / branching morphogenesis of an epithelial tube / endoplasmic reticulum-Golgi intermediate compartment / regulation of neurogenesis / hair follicle development / positive regulation of collagen biosynthetic process / spindle assembly / postsynaptic density, intracellular component / RNA processing / spleen development / positive regulation of endothelial cell migration / neuron projection morphogenesis / post-embryonic development / helicase activity / regulation of protein phosphorylation / lung development / multicellular organism growth / cerebral cortex development / rRNA processing / gene expression / regulation of inflammatory response / growth cone / 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 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 5.91 Å | |||||||||
データ登録者 | Zanova M / Zapletal D / Kubicek K / Stefl R / Pinkas M / Novacek J | |||||||||
資金援助 | チェコ, 2件
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引用 | ジャーナル: Mol Cell / 年: 2022 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 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_14854.map.gz | 45.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14854-v30.xml emd-14854.xml | 24.9 KB 24.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_14854.png | 28 KB | ||
Filedesc metadata | emd-14854.cif.gz | 7.9 KB | ||
その他 | emd_14854_additional_1.map.gz emd_14854_half_map_1.map.gz emd_14854_half_map_2.map.gz | 81.9 MB 86.6 MB 86.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14854 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14854 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_14854.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.835 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: Sharpened version of main EM map
ファイル | emd_14854_additional_1.map | ||||||||||||
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注釈 | Sharpened version of main EM map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_14854_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_14854_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Dicing state of mouse somatic dicer with pre-mir-15a
全体 | 名称: Dicing state of mouse somatic dicer with pre-mir-15a |
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要素 |
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-超分子 #1: Dicing state of mouse somatic dicer with pre-mir-15a
超分子 | 名称: Dicing state of mouse somatic dicer with pre-mir-15a タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all 詳細: TARBP2 present in the sample but its density was not observed in final 3D EM map |
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-超分子 #2: Dicing state of mouse somatic dicer
超分子 | 名称: Dicing state of mouse somatic dicer / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
-超分子 #3: Pre-mir-15a
超分子 | 名称: Pre-mir-15a / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
-分子 #1: Endoribonuclease Dicer
分子 | 名称: Endoribonuclease Dicer / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO / EC番号: ribonuclease III |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 226.925656 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MVWSHPQFEK GGGSGGGSGG SAWSHPQFEK GDYPYDVPDY AGTENLYFQG LVDMKSPALQ PLSMAGLQLM TPASSPMGPF FGLPWQQEA IHDNIYTPRK YQVELLEAAL DHNTIVCLNT GSGKTFIAVL LTKELAHQIR GDLNPHAKRT VFLVNSANQV A QQVSAVRT ...文字列: MVWSHPQFEK GGGSGGGSGG SAWSHPQFEK GDYPYDVPDY AGTENLYFQG LVDMKSPALQ PLSMAGLQLM TPASSPMGPF FGLPWQQEA IHDNIYTPRK YQVELLEAAL DHNTIVCLNT GSGKTFIAVL LTKELAHQIR GDLNPHAKRT VFLVNSANQV A QQVSAVRT HSDLKVGEYS DLEVNASWTK ERWSQEFTKH QVLIMTCYVA LTVLKNGYLS LSDINLLVFD ECHLAILDHP YR EIMKLCE SCPSCPRILG LTASILNGKC DPEELEEKIQ KLERILRSDA ETATDLVVLD RYTSQPCEIV VDCGPFTDRS GLY ERLLME LEAALDFIND CNVAVHSKER DSTLISKQIL SDCRAVLVVL GPWCADKVAG MMVRELQKYI KHEQEELHRK FLLF TDTLL RKIHALCEEY FSPASLDLKY VTPKVMKLLE ILRKYKPYER QQFESVEWYN NRNQDNYVSW SDSEDDDDDE EIEEK EKPE TNFPSPFTNI LCGIIFVERR YTAVVLNRLI KEAGKQDPEL AYISSNFITG HGIGKNQPRS KQMEAEFRKQ EEVLRK FRA HETNLLIATS VVEEGVDIPK CNLVVRFDLP TEYRSYVQSK GRARAPISNY VMLADTDKIK SFEEDLKTYK AIEKILR NK CSKSADGAEA DVHAGVDDED AFPPYVLRPD DGGPRVTINT AIGHINRYCA RLPSDPFTHL APKCRTRELP DGTFYSTL Y LPINSPLRAS IVGPPMDSVR LAERVVALIC CEKLHKIGEL DEHLMPVGKE TVKYEEELDL HDEEETSVPG RPGSTKRRQ CYPKAIPECL RESYPKPDQP CYLYVIGMVL TTPLPDELNF RRRKLYPPED TTRCFGILTA KPIPQIPHFP VYTRSGEVTI SIELKKSGF TLSQQMLELI TRLHQYIFSH ILRLEKPALE FKPTGAESAY CVLPLNVVND SGTLDIDFKF MEDIEKSEAR I GIPSTKYS KETPFVFKLE DYQDAVIIPR YRNFDQPHRF YVADVYTDLT PLSKFPSPEY ETFAEYYKTK YNLDLTNLNQ PL LDVDHTS SRLNLLTPRH LNQKGKALPL SSAEKRKAKW ESLQNKQILV PELCAIHPIP ASLWRKAVCL PSILYRLHCL LTA EELRAQ TASDAGVGVR SLPVDFRYPN LDFGWKKSID SKSFISSCNS SLAESDNYCK HSTTVVPEHA AHQGATRPSL ENHD QMSVN CKRLPAESPA KLQSEVSTDL TAINGLSYNK NLANGSYDLV NRDFCQGNQL NYFKQEIPVQ PTTSYPIQNL YNYEN QPKP SNECPLLSNT YLDGNANTST SDGSPAVSTM PAMMNAVKAL KDRMDSEQSP SVGYSSRTLG PNPGLILQAL TLSNAS DGF NLERLEMLGD SFLKHAITTY LFCTYPDAHE GRLSYMRSKK VSNCNLYRLG KKKGLPSRMV VSIFDPPVNW LPPGYVV NQ DKSNSEKWEK DEMTKDCLLA NGKLGEACEE EEDLTWRAPK EEAEDEDDFL EYDQEHIQFI DSMLMGSGAF VRKISLSP F SASDSAYEWK MPKKASLGSM PFASGLEDFD YSSWDAMCYL DPSKAVEEDD FVVGFWNPSE ENCGVDTGKQ SISYDLHTE QCIADKSIAD CVEALLGCYL TSCGERAAQL FLCSLGLKVL PVIKRTSREK ALDPAQENGS SQQKSLSGSC ASPVGPRSSA GKDLEYGCL KIPPRCMFDH PDAEKTLNHL ISGFETFEKK INYRFKNKAY LLQAFTHASY HYNTITDCYQ RLEFLGDAIL D YLITKHLY EDPRQHSPGV LTDLRSALVN NTIFASLAVK YDYHKYFKAV SPELFHVIDD FVKFQLEKNE MQGMDSELRR SE EDEEKEE DIEVPKAMGD IFESLAGAIY MDSGMSLEVV WQVYYPMMQP LIEKFSANVP RSPVRELLEM EPETAKFSPA ERT YDGKVR VTVEVVGKGK FKGVGRSYRI AKSAAARRAL RSLKANQPQV PNSGRGENLY FQGASDYKDH DGDYKDHDGS HHHH HHHH UniProtKB: Endoribonuclease Dicer |
-分子 #2: 59-nt precursor of miR-15a
分子 | 名称: 59-nt precursor of miR-15a / タイプ: rna / ID: 2 / コピー数: 1 |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 19.017279 KDa |
配列 | 文字列: UAGCAGCACA UAAUGGUUUG UGGAUGUUGA AAAGGUGCAG GCCAUACUGU GCUGCCUCA GENBANK: GENBANK: NR_029733.1 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.2 mg/mL | ||||||||||
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緩衝液 | pH: 8 構成要素:
詳細: The buffer was always prepared fresh in RNAse-free manner. | ||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV / 詳細: Described in STAR methods. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 検出モード: COUNTING / 実像数: 48253 / 平均電子線量: 60.198 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
初期モデル |
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詳細 | We used our previous deposition 7YYN as an initial model source. Initial local fitting was done using Chimera. ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide chain and distance restraints for polyribonucleotides. | ||||||
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 520 当てはまり具合の基準: Ramachandran Plot, Rotamer Analysis, Density Fit Analysis, Correlation coefficient | ||||||
得られたモデル | PDB-7zpi: |