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- EMDB-64765: Cryo-EM structure of DICER/26S-UG complex in dicing state -

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Basic information

Entry
Database: EMDB / ID: EMD-64765
TitleCryo-EM structure of DICER/26S-UG complex in dicing state
Map data
Sample
  • Complex: Complex of DICER/26S-UG in dicing state
    • RNA: RNA (64-MER)
    • Protein or peptide: Endoribonuclease Dicer
  • Ligand: CALCIUM ION
Keywordsendonuclease / miRNA / dicer / precursor miRNA / HYDROLASE
Function / homology
Function and homology information


peripheral nervous system myelin formation / global gene silencing by mRNA cleavage / negative regulation of Schwann cell proliferation / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / Small interfering RNA (siRNA) biogenesis / tRNA decay / apoptotic DNA fragmentation / ribonuclease III / deoxyribonuclease I activity ...peripheral nervous system myelin formation / global gene silencing by mRNA cleavage / negative regulation of Schwann cell proliferation / pre-miRNA binding / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / Small interfering RNA (siRNA) biogenesis / tRNA decay / apoptotic DNA fragmentation / ribonuclease III / deoxyribonuclease I activity / nerve development / positive regulation of Schwann cell differentiation / RISC-loading complex / positive regulation of myelination / miRNA metabolic process / RISC complex assembly / miRNA processing / ribonuclease III activity / pre-miRNA processing / siRNA processing / siRNA binding / M-decay: degradation of maternal mRNAs by maternally stored factors / Regulation of MITF-M-dependent genes involved in apoptosis / RISC complex / MicroRNA (miRNA) biogenesis / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / neuron projection morphogenesis / RNA endonuclease activity / helicase activity / double-stranded RNA binding / protein domain specific binding / negative regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / RNA binding / extracellular exosome / ATP binding / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Dicer, double-stranded RNA-binding domain / Dicer, partner-binding domain / Dicer, dsRNA-binding domain / : / : / Dicer, platform domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. ...Dicer, double-stranded RNA-binding domain / Dicer, partner-binding domain / Dicer, dsRNA-binding domain / : / : / Dicer, platform domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily / Dicer dimerisation domain / Dicer double-stranded RNA-binding fold domain profile. / Ribonuclease III family signature. / Ribonuclease III domain / Ribonuclease III family domain profile. / Ribonuclease III family / Ribonuclease III domain / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / 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 Dicer
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsNgo MK
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
Other government16103023 Hong Kong
CitationJournal: Nature / Year: 2026
Title: DICER cleavage fidelity is governed by 5'-end binding pockets.
Authors: Minh Khoa Ngo / Cong Truc Le / Tuan Anh Nguyen /
Abstract: RNA interference (RNAi) depends on DICER, an essential enzyme that processes RNA precursors into small regulatory RNAs. DICER cleaves RNA precursors according to the 5'-end counting rule, in which ...RNA interference (RNAi) depends on DICER, an essential enzyme that processes RNA precursors into small regulatory RNAs. DICER cleaves RNA precursors according to the 5'-end counting rule, in which RNA length is measured from the 5'-end. Previous work proposed a single 5'-end binding pocket that disfavours guanosine (5'-G), leading to cleavage inaccuracies. Here we show that 5'-G promotes precise cleavage for many substrates. Using massively parallel dicing assays and cryo-electron microscopy, we identify a conserved guanosine-favoured (G-favoured) binding pocket in DICER, distinct from the previously described uridine-favoured (U-favoured) pocket. Together, these pockets influence the alignment between 21-nucleotide and 22-nucleotide cleavage registers, expanding the mechanism of small-RNA biogenesis in metazoan DICERs. We also find that conflicts between 5'-end binding and RNA-motif recognition can trigger RNA conformational adjustments that preserve accurate cleavage-site selection. In addition, conformational adjustments of the double-stranded RNA-binding domain (dsRBD) and PAZ domain help to align substrates with the catalytic centres for precise double-strand cleavage. These results show that the DICER cleavage mechanism integrates dual 5'-end binding pockets, RNA-motif influence and domain motions, advancing our understanding of microRNA biogenesis.
History
DepositionMay 22, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64765.png

Downloads & links

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Map

FileDownload / File: emd_64765.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-0.0598758 - 1.8651757
Average (Standard dev.)0.0019291744 (±0.036133442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64765_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_64765_half_map_1.map
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Half map: #1

Fileemd_64765_half_map_2.map
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Sample components

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Entire : Complex of DICER/26S-UG in dicing state

EntireName: Complex of DICER/26S-UG in dicing state
Components
  • Complex: Complex of DICER/26S-UG in dicing state
    • RNA: RNA (64-MER)
    • Protein or peptide: Endoribonuclease Dicer
  • Ligand: CALCIUM ION

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Supramolecule #1: Complex of DICER/26S-UG in dicing state

SupramoleculeName: Complex of DICER/26S-UG in dicing state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Recombinant DICER and chemically synthesis shRNA forming complex in dicing-competent state
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RNA (64-MER)

MacromoleculeName: RNA (64-MER) / type: rna / ID: 1 / Details: 26S-UG / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 20.54525 KDa
SequenceString:
UGGAUAUUUC UCGCAGAUCU CAUGUGAAAA AAAAAACACA UGACAUCUGU GAGAAAUAUU CGUA

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Macromolecule #2: Endoribonuclease Dicer

MacromoleculeName: Endoribonuclease Dicer / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease III
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 217.989 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGHHHHHHHH HHPFFGLPWQ QEAIHDNIYT PRKYQVELLE AALDHNTIVC LNTGSGKTFI AVLLTKELSY QIRGDFSRNG KRTVFLVNS ANQVAQQVSA VRTHSDLKVG EYSNLEVNAS WTKERWNQEF TKHQVLIMTC YVALNVLKNG YLSLSDINLL V FDECHLAI ...String:
MGHHHHHHHH HHPFFGLPWQ QEAIHDNIYT PRKYQVELLE AALDHNTIVC LNTGSGKTFI AVLLTKELSY QIRGDFSRNG KRTVFLVNS ANQVAQQVSA VRTHSDLKVG EYSNLEVNAS WTKERWNQEF TKHQVLIMTC YVALNVLKNG YLSLSDINLL V FDECHLAI LDHPYREIMK LCENCPSCPR ILGLTASILN GKCDPEELEE KIQKLEKILK SNAETATDLV VLDRYTSQPC EI VVDCGPF TDRSGLYERL LMELEEALNF INDCNISVHS KERDSTLISK QILSDCRAVL VVLGPWCADK VAGMMVRELQ KYI KHEQEE LHRKFLLFTD TFLRKIHALC EEHFSPASLD LKFVTPKVIK LLEILRKYKP YERQQFESVE WYNNRNQDNY VSWS DSEDD DEDEEIEEKE KPETNFPSPF TNILCGIIFV ERRYTAVVLN RLIKEAGKQD PELAYISSNF ITGHGIGKNQ PRNKQ MEAE FRKQEEVLRK FRAHETNLLI ATSIVEEGVD IPKCNLVVRF DLPTEYRSYV QSKGRARAPI SNYIMLADTD KIKSFE EDL KTYKAIEKIL RNKCSKSVDT GETDIDPVMD DDDVFPPYVL RPDDGGPRVT INTAIGHINR YCARLPSDPF THLAPKC RT RELPDGTFYS TLYLPINSPL RASIVGPPMS CVRLAERVVA LICCEKLHKI GELDDHLMPV GKETVKYEEE LDLHDEEE T SVPGRPGSTK RRQCYPKAIP ECLRDSYPRP DQPCYLYVIG MVLTTPLPDE LNFRRRKLYP PEDTTRCFGI LTAKPIPQI PHFPVYTRSG EVTISIELKK SGFMLSLQML ELITRLHQYI FSHILRLEKP ALEFKPTDAD SAYCVLPLNV VNDSSTLDID FKFMEDIEK SEARIGIPST KYTKETPFVF KLEDYQDAVI IPRYRNFDQP HRFYVADVYT DLTPLSKFPS PEYETFAEYY K TKYNLDLT NLNQPLLDVD HTSSRLNLLT PRHLNQKGKA LPLSSAEKRK AKWESLQNKQ ILVPELCAIH PIPASLWRKA VC LPSILYR LHCLLTAEEL RAQTASDAGV GVRSLPADFR YPNLDFGWKK SIDSKSFISI SNSSSAENDN YCKHSTIVPE NAA HQGANR TSSLENHDQM SVNCRTLLSE SPGKLHVEVS ADLTAINGLS YNQNLANGSY DLANRDFCQG NQLNYYKQEI PVQP TTSYS IQNLYSYENQ PQPSDECTLL SNKYLDGNAN KSTSDGSPVM AVMPGTTDTI QVLKGRMDSE QSPSIGYSSR TLGPN PGLI LQALTLSNAS DGFNLERLEM LGDSFLKHAI TTYLFCTYPD AHEGRLSYMR SKKVSNCNLY RLGKKKGLPS RMVVSI FDP PVNWLPPGYV VNQDKSNTDK WEKDEMTKDC MLANGKLDED YEEEDEEEES LMWRAPKEEA DYEDDFLEYD QEHIRFI DN MLMGSGAFVK KISLSPFSTT DSAYEWKMPK KSSLGSMPFS SDFEDFDYSS WDAMCYLDPS KAVEEDDFVV GFWNPSEE N CGVDTGKQSI SYDLHTEQCI ADKSIADCVE ALLGCYLTSC GERAAQLFLC SLGLKVLPVI KRTDREKALC PTRENFNSQ QKNLSVSCAA ASVASSRSSV LKDSEYGCLK IPPRCMFDHP DADKTLNHLI SGFENFEKKI NYRFKNKAYL LQAFTHASYH YNTITDCYQ RLEFLGDAIL DYLITKHLYE DPRQHSPGVL TDLRSALVNN TIFASLAVKY DYHKYFKAVS PELFHVIDDF V QFQLEKNE MQGMDSELRR SEEDEEKEED IEVPKAMGDI FESLAGAIYM DSGMSLETVW QVYYPMMRPL IEKFSANVPR SP VRELLEM EPETAKFSPA ERTYDGKVRV TVEVVGKGKF KGVGRSYRIA KSAAARRALR SLKANQPQVP NS

UniProtKB: Endoribonuclease Dicer

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 3 / Number real images: 11242 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 84000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xw2

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 641317
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)

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Atomic model buiding 1

Initial modelPDB ID:

7xw2


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF ChimeraX (ver. 1.7)
RefinementProtocol: OTHER
Output model

PDB-9v43:
Cryo-EM structure of DICER/26S-UG complex in dicing state

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