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- EMDB-39321: DmDcr-2 with slm2 in intial binding state -

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Basic information

Entry
Database: EMDB / ID: EMD-39321
TitleDmDcr-2 with slm2 in intial binding state
Map data
Sample
  • Complex: DmDcr-2/LoqsPD/slm2 in initial binding state
    • Protein or peptide: Dicer-2
    • RNA: slm2
KeywordsRNAi / Dcr-2 / Loqs-PD / esiRNA / Cryo-EM / STRUCTURAL PROTEIN/RNA / STRUCTURAL PROTEIN-RNA complex
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.14 Å
AuthorsCao N / Su S / Wang J / Ma J / Wang H-W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural basis of endo-siRNA processing by Drosophila Dicer-2 and Loqs-PD.
Authors: Na Cao / Jia Wang / Ting Deng / Boming Fan / Shichen Su / Jinbiao Ma / Hong-Wei Wang /
Abstract: Endogenous small interfering RNAs (endo-siRNAs or esiRNAs) originate from either elongated endogenous transcripts capable of forming complex fold-back structures or from double-stranded regions ...Endogenous small interfering RNAs (endo-siRNAs or esiRNAs) originate from either elongated endogenous transcripts capable of forming complex fold-back structures or from double-stranded regions generated through intermolecular base pairing of convergently transcribed mRNAs. The mechanism of maturation and functionality of esiRNAs exhibit significant variation across diverse species. In Drosophila melanogaster, esiRNAs reside in both somatic and germline cells, where they serve as post-transcriptional modulators for specific target RNAs. Their maturation process critically relies on Dicer-2 (Dcr-2), with the assistance of its cofactor Loqs-PD. In this study, we have successfully elucidated the cryo-EM structures of Dcr-2/Loqs-PD complex bound to esiRNA precursors (pre-esiRNAs) in various states. Our structural and biochemical results reveal that ATP is essential for the cleavage of esiRNAs by the Dcr-2/Loqs-PD complex, a process analogous to the cleavage of double-stranded RNA (dsRNA). When Loqs-PD is present, pre-esiRNAs are preferentially loaded onto the Helicase domain of Dcr-2. Moreover, as the Helicase domain exhibits a preference for binding to the rigid end of double-stranded RNA, Dcr-2 tends to cleave pre-esiRNA from the small closed loop end, rather than the loose and flexible open end.
History
DepositionFeb 29, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39321.png

Downloads & links

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Map

FileDownload / File: emd_39321.map.gz / Format: CCP4 / Size: 52.7 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.)
1.08 Å/pix.
x 240 pix.
= 259.2 Å		1.08 Å/pix.
x 240 pix.
= 259.2 Å		1.08 Å/pix.
x 240 pix.
= 259.2 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.3516516 - 0.75288695
Average (Standard dev.)-0.0000053519143 (±0.03860774)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39321_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_39321_half_map_2.map
Projections & Slices
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Sample components

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Entire : DmDcr-2/LoqsPD/slm2 in initial binding state

EntireName: DmDcr-2/LoqsPD/slm2 in initial binding state
Components
  • Complex: DmDcr-2/LoqsPD/slm2 in initial binding state
    • Protein or peptide: Dicer-2
    • RNA: slm2

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Supramolecule #1: DmDcr-2/LoqsPD/slm2 in initial binding state

SupramoleculeName: DmDcr-2/LoqsPD/slm2 in initial binding state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Dicer-2

MacromoleculeName: Dicer-2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EDVEIKPRGY QLRLVDHLTK SNGIVYLPTG SGKTFVAILV LKRFSQDFDK PIESGGKRAL FMCNTVELAR QQAMAVRRCT NFKVGFYVG EQGVDDWTRG MWSDEIKKNQ VLVGTAQVFL DMVTQTYVAL SSLSVVIIDE CHHGTGHHPF REFMRLFTIA N QTKLPRVV ...String:
EDVEIKPRGY QLRLVDHLTK SNGIVYLPTG SGKTFVAILV LKRFSQDFDK PIESGGKRAL FMCNTVELAR QQAMAVRRCT NFKVGFYVG EQGVDDWTRG MWSDEIKKNQ VLVGTAQVFL DMVTQTYVAL SSLSVVIIDE CHHGTGHHPF REFMRLFTIA N QTKLPRVV GLTGVLIKGN EITNVATKLK ELEITYRGNI ITVSDTKEME NVMLYATKPT EVMVSFPHQE QVLTVTRLIS AE IEKFYVS LDLMNIGVQP IRRSKSLQCL RDPSKKSFVK QLFNDFLYQM KEYGIYAASI AIISLIVEFD IKRRQAETLS VKL MHRTAL TLCEKIRHLL VQKLQDMTYD DDDDNVNTEE VIMNFSTPKV QRFLMSLKVS FADKDPKDIC CLVFVERRYT CKCI YGLLL NYIQSTPELR NVLTPQFMVG RNNISPDFES VLERKWQKSA IQQFRDGNAN LMICSSVLEE GIDVQACNHV FILDP VKTF NMYVQSKGRA RTTEAKFVLF TADKEREKTI QQIYQYRKAH NDIAEYLKDR VLEKTEPELY EIKGHFQDDI DPFTNE NGA VLLPNNALAI LHRYCQTIPT DAFGFVIPWF HVLQEDERDR IFGVSAKGKH VISINMPVNC MLRDTIYSDP MDNVKTA KI SAAFKACKVL YSLGELNERF VPKTLKERVA SIADVHFEHW NKYGDSVTAT VNKADKSKDR TYKTECPLEF YDALPRVG E ICYAYEIFLE PQFESCEYTE HMYLNLQTPR NYAILLRNKL PRLAEMPLFS NQGKLHVRVA NAPLEVIIQN SEQLELLHQ FHGMVFRDIL KIWHPFFVLD RRSKENSYLV VPLILGAGEQ KCFDWELMTN FRRLPQSHGS NVQQREQQPA PRPEDFEGKI VTQWYANYD KPMLVTKVHR ELTPLSYMEK NQQDKTYYEF TMSKYGNRIG DVVHKDKFMI EVRDLTEQLT FYVHNRGKFN A KSKAKMKV ILIPELCFNF NFPGDLWLKL IFLPSILNRM YFLLHAEALR KRFNTYLNLH LLPFNGTDYM PRPLEIDYSL KR NVDPLGN VIPTEDIEEP KSLLEPMPTK SIEASVANLE ITEFENPWQK YMEPVDLSRN LLSTYPVELD YYYHFSVGNV CEM NEMDFE DKEYWAKNQF HMPTGNIYGN RTPAKTNANV PALMPSKPTV RGKVKPLLIL QKTVSKEHIT PAEQGEFLAA ITAS SAADV FDMERLEILG NSFLKLSATL YLASKYSDWN EGTLTEVKSK LVSNRNLLFC LIDADIPKTL NTIQFTPRYT WLPPG ISLP HNVLALWREN PEFAKIIGPH NLRDLALGDE ESLVKGNCSD INYNRFVEGC RANGQSFYAG ADFSSEVNFC VGLVTI PNK VIADTLEALL GVIVKNYGLQ HAFKMLEYFK ICRADIDKPL TQLLNLELGG KKMRANVNTT EIDGFLINHY YLEKNLG YT FKDRRYLLQA LTHPSYPTNR ITGSYQELEF IGNAILDFLI SAYIFENNTK MNPGALTDLR SALVNNTTLA CICVRHRL H FFILAENAKL SEIISKFVNF QESQGHRVTN YVRILLEEAD VQPTPLDLDD ELDMTELPHA NKCISQEAEK GVPPKGEFN MSTNVDVPKA LGDVLEALIA AVYLDCRDLQ RTWEVIFNLF EPELQEFTRK VPINHIRQLV EHKHAKPVFS SPIVEGETVM VSCQFTCME KTIKVYGFGS NKDQAKLSAA KHALQQLSKC DA

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Macromolecule #2: slm2

MacromoleculeName: slm2 / type: rna / ID: 2
Source (natural)Organism: Drosophila melanogaster (fruit fly)
SequenceString:
GGUUCGCUCC CGGCGCUUCA CAGGCGCUGG AAAAUCUUAA CCGCCGGAAG UCACUUCCGC UGGCUUUGAU UUUCCAGCGU CUGUCGAGCG GAAGGAGGGA CCUU

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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

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
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: 6.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 52187
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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