+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31741 | |||||||||
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Title | Structure of the Dicer-2-R2D2 heterodimer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA binding protein / Ribonuclease / Double-stranded RNA-binding protein | |||||||||
Function / homology | Function and homology information follicle cell of egg chamber stalk formation / lncRNA catabolic process / : / positive regulation of Toll signaling pathway / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome ...follicle cell of egg chamber stalk formation / lncRNA catabolic process / : / positive regulation of Toll signaling pathway / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / dsRNA transport / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage / ribonuclease III / apoptotic DNA fragmentation / deoxyribonuclease I activity / RISC-loading complex / detection of virus / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / ribonuclease III activity / siRNA binding / siRNA processing / ATP-dependent activity, acting on RNA / positive regulation of innate immune response / RISC complex / positive regulation of defense response to virus by host / helicase activity / locomotory behavior / mRNA 3'-UTR binding / heterochromatin formation / cellular response to virus / cytoplasmic ribonucleoprotein granule / double-stranded RNA binding / defense response to virus / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Yamaguchi S / Nishizawa T / Kusakizako T / Yamashita K / Tomita A / Hirano H / Nishimasu H / Nureki O | |||||||||
Funding support | Japan, 1 items
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Citation | Journal: Nature / Year: 2022 Title: Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex. Authors: Sonomi Yamaguchi / Masahiro Naganuma / Tomohiro Nishizawa / Tsukasa Kusakizako / Yukihide Tomari / Hiroshi Nishimasu / Osamu Nureki / Abstract: In flies, Argonaute2 (Ago2) and small interfering RNA (siRNA) form an RNA-induced silencing complex to repress viral transcripts. The RNase III enzyme Dicer-2 associates with its partner protein R2D2 ...In flies, Argonaute2 (Ago2) and small interfering RNA (siRNA) form an RNA-induced silencing complex to repress viral transcripts. The RNase III enzyme Dicer-2 associates with its partner protein R2D2 and cleaves long double-stranded RNAs to produce 21-nucleotide siRNA duplexes, which are then loaded into Ago2 in a defined orientation. Here we report cryo-electron microscopy structures of the Dicer-2-R2D2 and Dicer-2-R2D2-siRNA complexes. R2D2 interacts with the helicase domain and the central linker of Dicer-2 to inhibit the promiscuous processing of microRNA precursors by Dicer-2. Notably, our structure represents the strand-selection state in the siRNA-loading process, and reveals that R2D2 asymmetrically recognizes the end of the siRNA duplex with the higher base-pairing stability, and the other end is exposed to the solvent and is accessible by Ago2. Our findings explain how R2D2 senses the thermodynamic asymmetry of the siRNA and facilitates the siRNA loading into Ago2 in a defined orientation, thereby determining which strand of the siRNA duplex is used by Ago2 as the guide strand for target silencing. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31741.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-31741-v30.xml emd-31741.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31741_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_31741.png | 66 KB | ||
Masks | emd_31741_msk_1.map | 20.8 MB | Mask map | |
Filedesc metadata | emd-31741.cif.gz | 6.6 KB | ||
Others | emd_31741_half_map_1.map.gz emd_31741_half_map_2.map.gz | 17.6 MB 17.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31741 | HTTPS FTP |
-Validation report
Summary document | emd_31741_validation.pdf.gz | 793 KB | Display | EMDB validaton report |
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Full document | emd_31741_full_validation.pdf.gz | 792.6 KB | Display | |
Data in XML | emd_31741_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | emd_31741_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31741 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31741 | HTTPS FTP |
-Related structure data
Related structure data | 7v6bMC 7v6cC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11099 (Title: Structure of the Dicer-2-R2D2 heterodimer bound to a small RNA duplex Data size: 1.4 TB Data #1: Structure of the Dicer-2-R2D2 heterodimer [micrographs - multiframe] Data #2: Structure of the Dicer-2-R2D2 heterodimer bound to small RNA duplex [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31741.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_31741_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31741_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31741_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dicer-2-R2D2
Entire | Name: Dicer-2-R2D2 |
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Components |
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-Supramolecule #1: Dicer-2-R2D2
Supramolecule | Name: Dicer-2-R2D2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: Dicer-2, isoform A
Macromolecule | Name: Dicer-2, isoform A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 198.134734 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GSMEDVEIKP RGYQLRLVDH LTKSNGIVYL PTGSGKTFVA ILVLKRFSQD FDKPIESGGK RALFMCNTVE LARQQAMAVR RCTNFKVGF YVGEQGVDDW TRGMWSDEIK KNQVLVGTAQ VFLDMVTQTY VALSSLSVVI IDECHHGTGH HPFREFMRLF T IANQTKLP ...String: GSMEDVEIKP RGYQLRLVDH LTKSNGIVYL PTGSGKTFVA ILVLKRFSQD FDKPIESGGK RALFMCNTVE LARQQAMAVR RCTNFKVGF YVGEQGVDDW TRGMWSDEIK KNQVLVGTAQ VFLDMVTQTY VALSSLSVVI IDECHHGTGH HPFREFMRLF T IANQTKLP RVVGLTGVLI KGNEITNVAT KLKELEITYR GNIITVSDTK ELENVMLYAT KPTEVMVSFP HQEQVLTVTR LI SAEIEKF YVSLDLMNIG VQPIRRSKSL QCLRDPSKKS FVKQLFNDFL YQMKEYGIYA ASIAIISLIV EFDIKRRQAE TLS VKLMHR TALTLCEKIR HLLVQKLQDM TYDDDDDNVN TEEVIMNFST PKVQRFLMSL KVSFADKDPK DICCLVFVER RYTC KCIYG LLLNYIQSTP ELRNVLTPQF MVGRNNISPD FESVLERKWQ KSAIQQFRDG NANLMICSSV LEEGIDVQAC NHVFI LDPV KTFNMYVQSK GRARTTEAKF VLFTADKERE KTIQQIYQYR KAHNDIAEYL KDRVLEKTEP ELYEIKGHFQ DDIDPF TNE NGAVLLPNNA LAILHRYCQT IPTDAFGFVI PWFHVLQEDE RDRIFGVSAK GKHVISINMP VNCMLRDTIY SDPMDNV KT AKISAAFKAC KVLYSLGELN ERFVPKTLKE RVASIADVHF EHWNKYGDSV TATVNKADKS KDRTYKTECP LEFYDALP R VGEICYAYEI FLEPQFESCE YTEHMYLNLQ TPRNYAILLR NKLPRLAEMP LFSNQGKLHV RVANAPLEVI IQNSEQLEL LHQFHGMVFR DILKIWHPFF VLDRRSKENS YLVVPLILGA GEQKCFDWEL MTNFRRLPQS HGSNVQQREQ QPAPRPEDFE GKIVTQWYA NYDKPMLVTK VHRELTPLSY MEKNQQDKTY YEFTMSKYGN RIGDVVHKDK FMIEVRDLTE QLTFYVHNRG K FNAKSKAK MKVILIPELC FNFNFPGDLW LKLIFLPSIL NRMYFLLHAE ALRKRFNTYL NLHLLPFNGT DYMPRPLEID YS LKRNVDP LGNVIPTEDI EEPKSLLEPM PTKSIEASVA NLEITEFENP WQKYMEPVDL SRNLLSTYPV ELDYYYHFSV GNV CEMNEM DFEDKEYWAK NQFHMPTGNI YGNRTPAKTN ANVPALMPSK PTVRGKVKPL LILQKTVSKE HITPAEQGEF LAAI TASSA ADVFDMERLE ILGDSFLKLS ATLYLASKYS DWNEGTLTEV KSKLVSNRNL LFCLIDADIP KTLNTIQFTP RYTWL PPGI SLPHNVLALW RENPEFAKII GPHNLRDLAL GDEESLVKGN CSDINYNRFV EGCRANGQSF YAGADFSSEV NFCVGL VTI PNKVIADTLE ALLGVIVKNY GLQHAFKMLE YFKICRADID KPLTQLLNLE LGGKKMRANV NTTEIDGFLI NHYYLEK NL GYTFKDRRYL LQALTHPSYP TNRITGSYQE LEFIGDAILD FLISAYIFEN NTKMNPGALT DLRSALVNNT TLACICVR H RLHFFILAEN AKLSEIISKF VNFQESQGHR VTNYVRILLE EADVQPTPLD LDDELDMTEL PHANKCISQE AEKGVPPKG EFNMSTNVDV PKALGDVLEA LIAAVYLDCR DLQRTWEVIF NLFEPELQEF TRKVPINHIR QLVEHKHAKP VFSSPIVEGE TVMVSCQFT CMEKTIKVYG FGSNKDQAKL SAAKHALQQL SKCDA UniProtKB: Endoribonuclease Dcr-2 |
-Macromolecule #2: R2D2
Macromolecule | Name: R2D2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 35.517699 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GPFTMDNKSA VSALQEFCAR TQINLPTYSF IPGEDGGYVC KVELLEIEAL GNGRSKRDAK HLAASNILRK IQLLPGIHGL MKDSTVGDL DEELTNLNRD MVKELRDYCV RREMPLPCIE VVQQSGTPSA PEFVACCSVA SIVRYGKSDK KKDARQRAAI E MLALISSN ...String: GPFTMDNKSA VSALQEFCAR TQINLPTYSF IPGEDGGYVC KVELLEIEAL GNGRSKRDAK HLAASNILRK IQLLPGIHGL MKDSTVGDL DEELTNLNRD MVKELRDYCV RREMPLPCIE VVQQSGTPSA PEFVACCSVA SIVRYGKSDK KKDARQRAAI E MLALISSN SDNLRPDQMQ VASTSKLKVV DMEESMEELE ALRRKKFTTY WELKEAGSVD HTGMRLCDRH NYFKNFYPTL KK EAIEAIN SDEYESSKDK AMDVMSSLKI TPKISEVESS SLVPLLSVEL NCAFDVVLMA KETDIYDHII DYFRTMLI UniProtKB: LD06392p |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |