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- EMDB-27415: Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partne... -
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Open data
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Basic information
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Title | Structural Basis of MicroRNA Biogenesis by Dicer-1 and Its Partner Protein Loqs-PB - complex IIa | ||||||||||||
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![]() | Dicer / Dcr-1 / Loquacious / Loqs-P / miRNA / RNA BINDING PROTEIN-RNA complex | ||||||||||||
Function / homology | ![]() mitotic cell cycle, embryonic / germarium-derived female germ-line cyst formation / germarium-derived oocyte fate determination / germ-line stem cell division / : / MicroRNA (miRNA) biogenesis / pole cell formation / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / segment polarity determination ...mitotic cell cycle, embryonic / germarium-derived female germ-line cyst formation / germarium-derived oocyte fate determination / germ-line stem cell division / : / MicroRNA (miRNA) biogenesis / pole cell formation / Small interfering RNA (siRNA) biogenesis / female germ-line stem cell asymmetric division / segment polarity determination / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome / RISC complex binding / pre-miRNA binding / germ-line stem cell population maintenance / ribonuclease III / apoptotic DNA fragmentation / deoxyribonuclease I activity / RISC-loading complex / miRNA metabolic process / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / miRNA processing / pre-miRNA processing / siRNA binding / siRNA processing / RISC complex / dendrite morphogenesis / response to starvation / RNA endonuclease activity / helicase activity / central nervous system development / double-stranded RNA binding / single-stranded RNA binding / RNA binding / ATP binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.06 Å | ||||||||||||
![]() | Jouravleva K / Golovenko D / Demo G / Dutcher RC / Tanaka Hall TM / Zamore PD / Korostelev AA | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Authors: Karina Jouravleva / Dmitrij Golovenko / Gabriel Demo / Robert C Dutcher / Traci M Tanaka Hall / Phillip D Zamore / Andrei A Korostelev / ![]() ![]() Abstract: In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM ...In animals and plants, Dicer enzymes collaborate with double-stranded RNA-binding domain (dsRBD) proteins to convert precursor-microRNAs (pre-miRNAs) into miRNA duplexes. We report six cryo-EM structures of Drosophila Dicer-1 that show how Dicer-1 and its partner Loqs‑PB cooperate (1) before binding pre-miRNA, (2) after binding and in a catalytically competent state, (3) after nicking one arm of the pre-miRNA, and (4) following complete dicing and initial product release. Our reconstructions suggest that pre-miRNA binds a rare, open conformation of the Dicer‑1⋅Loqs‑PB heterodimer. The Dicer-1 dsRBD and three Loqs‑PB dsRBDs form a tight belt around the pre-miRNA, distorting the RNA helix to place the scissile phosphodiester bonds in the RNase III active sites. Pre-miRNA cleavage shifts the dsRBDs and partially closes Dicer-1, which may promote product release. Our data suggest a model for how the Dicer‑1⋅Loqs‑PB complex affects a complete cycle of pre-miRNA recognition, stepwise endonuclease cleavage, and product release. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 141.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.5 KB 20.5 KB | Display Display | ![]() |
Images | ![]() | 73.1 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() | 139.3 MB 139.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dfvMC ![]() 8dg5C ![]() 8dg7C ![]() 8dgaC ![]() 8dgiC ![]() 8dgjC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27415_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27415_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Ternary complex of Dicer-1 and Loqs-PB binding pre-miRNA
Entire | Name: Ternary complex of Dicer-1 and Loqs-PB binding pre-miRNA |
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Components |
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-Supramolecule #1: Ternary complex of Dicer-1 and Loqs-PB binding pre-miRNA
Supramolecule | Name: Ternary complex of Dicer-1 and Loqs-PB binding pre-miRNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Endoribonuclease Dcr-1
Macromolecule | Name: Endoribonuclease Dcr-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 255.733797 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MAFHWCDNNL HTTVFTPRDF QVELLATAYE RNTIICLGHR SSKEFIALKL LQELSRRARR HGRVSVYLSC EVGTSTEPCS IYTMLTHLT DLRVWQEQPD MQIPFDHCWT DYHVSILRPE GFLYLLETRE LLLSRVELIV LEDCHDSAVY QRIRPLFENH I MPAPPADR ...String: MAFHWCDNNL HTTVFTPRDF QVELLATAYE RNTIICLGHR SSKEFIALKL LQELSRRARR HGRVSVYLSC EVGTSTEPCS IYTMLTHLT DLRVWQEQPD MQIPFDHCWT DYHVSILRPE GFLYLLETRE LLLSRVELIV LEDCHDSAVY QRIRPLFENH I MPAPPADR PRILGLAGPL HSAGCELQQL SAMLATLEQS VLCQIESASD IVTVLRYCSR PHEYIVQCAP FEMDELSLVL AD VLNTHKS FLLDHRYDPY EIYGTDQFMD ELKDIPDPKV DPLNVINSLL VVLHEMGPWC TQRAAHHFYQ CNEKLKVKTP HER HYLLYC LVSTALIQLY SLCEHAFHRH LGSGSDSRQT IERYSSPKVR RLLQTLRCFK PEEVHTQADG LRRMRHQVDQ ADFN RLSHT LESKCRMVDQ LDQPPTETRA LVATLEQILH TTEDRQTNRS AARVTPTPTP AHAKPKPSSG ANTAQPRTRR RVYTR RHHR DHNDGSDTLC ALIYCNQNHT ARVLFELLAE ISRRDPDLKF LRCQYTTDRV ADPTTEPKEA ELEHRRQEEV LKRFRM HDC NVLIGTSVLE EGIDVPKCNL VVRWDPPTTY RSYVQCKGRA RAAPAYHVIL VAPSYKSPTV GSVQLTDRSH RYICATG DT TEADSDSDDS AMPNSSGSDP YTFGTARGTV KILNPEVFSK QPPTACDIKL QEIQDELPAS AQLDTSNSSD EAVSMSNT S PSESSTEQKS RRFQCELSSL TEPEDTSDTT AEIDTAHSLA STTKDLVHQM AQYREIEQML LSKCANTEPP EQEQCEAER FSACLAAYRP KPHLLTGASV DLGSAIALVN KYCARLPSDT FTKLTALWRC TRNERAGVTL FQYTLRLPIN SPLKHDIVGL PMPTQTLAR RLAALQACVE LHRIGELDDQ LQPIGKEGFR ALEPDWECFE LEPEDEQIVQ LSDEPRPGTT KRRQYYYKRI A SEFCDCRP VAGAPCYLYF IQLTLQCPIP EEQNTRGRKI YPPEDAQQGF GILTTKRIPK LSAFSIFTRS GEVKVSLELA KE RVILTSE QIVCINGFLN YTFTNVLRLQ KFLMLFDPDS TENCVFIVPT VKAPAGGKHI DWQFLELIQA NGNTMPRAVP DEE RQAQPF DPQRFQDAVV MPWYRNQDQP QYFYVAEICP HLSPLSCFPG DNYRTFKHYY LVKYGLTIQN TSQPLLDVDH TSAR LNFLT PRYVNRKGVA LPTSSEETKR AKRENLEQKQ ILVPELCTVH PFPASLWRTA VCLPCILYRI NGLLLADDIR KQVSA DLGL GRQQIEDEDF EWPMLDFGWS LSEVLKKSRE SKQKESLKDD TINGKDLVDV EKKAISEETQ IDKDSKDDKV EKSAIE LII EGEEKLQEAD DFIEIGTWSN DMADDIASFN QEDDDEDDAF HLPVLPANVK FCDQQTRYGS PTFWDVSNGE SGFKGPK SS QNKQGGKGKA KGPAKPTFNY YDSDNSLGSS YDDDDNAGPL NYMHHNYSSD DDDVADDIDA GRIAFTSKNE AETIETAQ E VEKRQKQLSI IQATNANERQ YQQTKNLLIG FNFKHEDQKE PATIRYEESI AKLKTEIESG GMLVPHDQQL VLKRSDAAE AQVAKVSMME LLKQLLPYVN EDVLAKKLGD RRELLLSDLV ELNADWVARH EQETYNVMGC GDSFDNYNDH HRLNLDEKQL KLQYERIEI EPPTSTKAIT SAILPAGFSF DRQPDLVGHP GPSPSIILQA LTMSNANDGI NLERLETIGD SFLKYAITTY L YITYENVH EGKLSHLRSK QVANLNLYRL GRRKRLGEYM IATKFEPHDN WLPPCYYVPK ELEKALIEAK IPTHHWKLAD LL DIKNLSS VQICEMVREK ADALGLEQNG GAQNGQLDDS NDSCNDFSCF IPYNLVSQHS IPDKSIADCV EALIGAYLIE CGP RGALLF MAWLGVRVLP ITRQLDGGNQ EQRIPGSTKP NAENVVTVYG AWPTPRSPLL HFAPNATEEL DQLLSGFEEF EESL GYKFR DRSYLLQAMT HASYTPNRLT DCYQRLEFLG DAVLDYLITR HLYEDPRQHS PGALTDLRSA LVNNTIFASL AVRHG FHKF FRHLSPGLND VIDRFVRIQQ ENGHCISEEY YLLSEEECDD AEDVEVPKAL GDVFESIAGA IFLDSNMSLD VVWHVY SNM MSPEIEQFSN SVPKSPIREL LELEPETAKF GKPEKLADGR RVRVTVDVFC KGTFRGIGRN YRIAKCTAAK CALRQLK KQ GLIAKKD UniProtKB: Endoribonuclease Dcr-1 |
-Macromolecule #3: Loquacious, isoform B
Macromolecule | Name: Loquacious, isoform B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 50.149867 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MDQENFHGSS LPQQLQNLHI QPQQASPNPV QTGFAPRRHY NNLVGLGNGN AVSGSPVKGA PLGQRHVKLK KEKISAQVAQ LSQPGQLQL SDVGDPALAG GSGLQGGVGL MGVILPSDEA LKFVSETDAN GLAMKTPVSI LQELLSRRGI TPGYELVQIE G AIHEPTFR ...String: MDQENFHGSS LPQQLQNLHI QPQQASPNPV QTGFAPRRHY NNLVGLGNGN AVSGSPVKGA PLGQRHVKLK KEKISAQVAQ LSQPGQLQL SDVGDPALAG GSGLQGGVGL MGVILPSDEA LKFVSETDAN GLAMKTPVSI LQELLSRRGI TPGYELVQIE G AIHEPTFR FRVSFKDKDT PFTAMGAGRS KKEAKHAAAR ALIDKLIGAQ LPESPSSSAG PSVTGLTVAG SGGDGNANAT GG GDASDKT VGNPIGWLQE MCMQRRWPPP SYETETEVGL PHERLFTIAC SILNYREMGK GKSKKIAKRL AAHRMWMRLQ ETP IDSGKI SDSICGELEG EPRSSENYYG ELKDISVPTL TTQHSNKVSQ FHKTLKNATG KKLLKLQKTC LKNNKIDYIK LLGE IATEN QFEVTYVDIE EKTFSGQFQC LVQLSTLPVG VCHGSGPTAA DAQRHAAQNA LEYLKIMTKK UniProtKB: Protein Loquacious |
-Macromolecule #2: RNA (60-MER)
Macromolecule | Name: RNA (60-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 19.102305 KDa |
Sequence | String: UGAGGUAGUA GGUUGUAUAG UAGUAAUUAC ACAUCAUACU AUACAACCUA CUACCUCUCU |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 2D array |
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Sample preparation
Buffer | pH: 7.9 / Component - Concentration: 20.0 mM / Component - Formula: HEPES-KOH / Component - Name: HEPES-KOH |
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Grid | Model: C-flat-1.2/1.3 / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |