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- EMDB-31741: Structure of the Dicer-2-R2D2 heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-31741
TitleStructure of the Dicer-2-R2D2 heterodimer
Map data
Sample
  • Complex: Dicer-2-R2D2
    • Protein or peptide: Dicer-2, isoform A
    • Protein or peptide: R2D2
KeywordsRNA binding protein / Ribonuclease / Double-stranded RNA-binding protein
Function / homology
Function and homology information


follicle cell of egg chamber stalk formation / positive regulation of Toll signaling pathway / lncRNA catabolic process / MicroRNA (miRNA) biogenesis / RNAi-mediated antiviral immune response / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage ...follicle cell of egg chamber stalk formation / positive regulation of Toll signaling pathway / lncRNA catabolic process / MicroRNA (miRNA) biogenesis / RNAi-mediated antiviral immune response / Small interfering RNA (siRNA) biogenesis / PKR-mediated signaling / regulation of regulatory ncRNA processing / dosage compensation by hyperactivation of X chromosome / global gene silencing by mRNA cleavage / apoptotic DNA fragmentation / ribonuclease III / deoxyribonuclease I activity / RISC-loading complex / detection of virus / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / ribonuclease III activity / siRNA processing / siRNA binding / ATP-dependent activity, acting on RNA / RISC complex / positive regulation of innate immune response / positive regulation of defense response to virus by host / mRNA 3'-UTR binding / helicase activity / locomotory behavior / cellular response to virus / cytoplasmic ribonucleoprotein granule / heterochromatin formation / double-stranded RNA binding / defense response to virus / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / : / Dicer, platform domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family ...: / : / Dicer, platform domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Endoribonuclease Dcr-2 / LD06392p
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYamaguchi S / Nishizawa T / Kusakizako T / Yamashita K / Tomita A / Hirano H / Nishimasu H / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)202111067 Japan
CitationJournal: 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
DepositionAug 20, 2021-
Header (metadata) releaseMar 23, 2022-
Map releaseMar 23, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31741.png

Downloads & links

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Map

FileDownload / File: emd_31741.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 176 pix.
= 219.12 Å		1.25 Å/pix.
x 176 pix.
= 219.12 Å		1.25 Å/pix.
x 176 pix.
= 219.12 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.14640076 - 0.25994143
Average (Standard dev.)0.0003070644 (±0.006948173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 219.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_31741_msk_1.map
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Half map: #2

Fileemd_31741_half_map_1.map
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Half map: #1

Fileemd_31741_half_map_2.map
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Sample components

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Entire : Dicer-2-R2D2

EntireName: Dicer-2-R2D2
Components
  • Complex: Dicer-2-R2D2
    • Protein or peptide: Dicer-2, isoform A
    • Protein or peptide: R2D2

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Supramolecule #1: Dicer-2-R2D2

SupramoleculeName: Dicer-2-R2D2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Dicer-2, isoform A

MacromoleculeName: Dicer-2, isoform A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 198.134734 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: R2D2

MacromoleculeName: R2D2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 35.517699 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144979
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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