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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Mouse endoribonuclease Dicer (composite structure) | |||||||||
![]() | combined map from the locally refined parts of the protein | |||||||||
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![]() | endoribonuclease / gene silencing / post-transcriptional / catalytic enzyme / cytoplasm / RNA BINDING PROTEIN | |||||||||
Function / homology | ![]() regulation of muscle cell apoptotic process / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / ganglion development / hair follicle cell proliferation / zygote asymmetric cell division / regulation of oligodendrocyte differentiation / cardiac neural crest cell development involved in outflow tract morphogenesis / olfactory bulb interneuron differentiation / regulation of odontogenesis of dentin-containing tooth ...regulation of muscle cell apoptotic process / MicroRNA (miRNA) biogenesis / Small interfering RNA (siRNA) biogenesis / ganglion development / hair follicle cell proliferation / zygote asymmetric cell division / regulation of oligodendrocyte differentiation / cardiac neural crest cell development involved in outflow tract morphogenesis / olfactory bulb interneuron differentiation / regulation of odontogenesis of dentin-containing tooth / trophectodermal cell proliferation / regulation of enamel mineralization / regulation of miRNA metabolic process / peripheral nervous system myelin formation / regulation of epithelial cell differentiation / regulation of RNA metabolic process / spermatogonial cell division / global gene silencing by mRNA cleavage / spinal cord motor neuron differentiation / negative regulation of Schwann cell proliferation / epidermis morphogenesis / reproductive structure development / ribonuclease III / regulation of Notch signaling pathway / myoblast differentiation involved in skeletal muscle regeneration / nerve development / positive regulation of myelination / positive regulation of Schwann cell differentiation / regulation of regulatory T cell differentiation / meiotic spindle organization / RISC-loading complex / intestinal epithelial cell development / RISC complex assembly / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA processing / ribonuclease III activity / pre-miRNA processing / pericentric heterochromatin formation / siRNA processing / regulation of stem cell differentiation / regulation of viral genome replication / RISC complex / mRNA stabilization / inner ear receptor cell development / cartilage development / digestive tract development / embryonic hindlimb morphogenesis / embryonic limb morphogenesis / cardiac muscle cell development / positive regulation of miRNA metabolic process / miRNA binding / regulation of neuron differentiation / regulation of myelination / negative regulation of glial cell proliferation / hair follicle morphogenesis / stem cell population maintenance / branching morphogenesis of an epithelial tube / hair follicle development / regulation of neurogenesis / postsynaptic density, intracellular component / RNA processing / spindle assembly / spleen development / neuron projection morphogenesis / post-embryonic development / lung development / helicase activity / cerebral cortex development / multicellular organism growth / rRNA processing / regulation of gene expression / regulation of inflammatory response / angiogenesis / defense response to virus / gene expression / cell population proliferation / regulation of cell cycle / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.84 Å | |||||||||
![]() | Zanova M / Zapletal D / Kubicek K / Stefl R / Pinkas M / Novacek J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and functional basis of mammalian microRNA biogenesis by Dicer. Authors: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / ...Authors: David Zapletal / Eliska Taborska / Josef Pasulka / Radek Malik / Karel Kubicek / Martina Zanova / Christian Much / Marek Sebesta / Valeria Buccheri / Filip Horvat / Irena Jenickova / Michaela Prochazkova / Jan Prochazka / Matyas Pinkas / Jiri Novacek / Diego F Joseph / Radislav Sedlacek / Carrie Bernecky / Dónal O'Carroll / Richard Stefl / Petr Svoboda / ![]() ![]() ![]() ![]() ![]() Abstract: MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is ...MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucleases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is specifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer's DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the complete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicer•-miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleavage-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 202 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.1 KB 28.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 79.7 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Others | ![]() ![]() ![]() ![]() ![]() | 192.5 MB 170.2 MB 107.1 MB 178.8 MB 178.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yz4MC ![]() 7yymC ![]() 7yynC ![]() 7zpiC ![]() 7zpjC ![]() 7zpkC C: citing same article ( M: atomic model generated by this map |
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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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Annotation | combined map from the locally refined parts of the protein | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: locally refined part of the protein
File | emd_14387_additional_1.map | ||||||||||||
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Annotation | locally refined part of the protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: locally refined part of the protein
File | emd_14387_additional_2.map | ||||||||||||
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Annotation | locally refined part of the protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: EM map of the whole protein, before local refinement
File | emd_14387_additional_3.map | ||||||||||||
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Annotation | EM map of the whole protein, before local refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_14387_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_14387_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Free form of mouse somatic dicer
Entire | Name: Free form of mouse somatic dicer |
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Components |
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-Supramolecule #1: Free form of mouse somatic dicer
Supramolecule | Name: Free form of mouse somatic dicer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Endoribonuclease Dicer
Macromolecule | Name: Endoribonuclease Dicer / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease III |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 226.809594 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MVWSHPQFEK GGGSGGGSGG SAWSHPQFEK GDYPYDVPDY AGTENLYFQG LVDMKSPALQ PLSMAGLQLM TPASSPMGPF FGLPWQQEA IHDNIYTPRK YQVELLEAAL DHNTIVCLNT GSGKTFIAVL LTKELAHQIR GDLNPHAKRT VFLVNSANQV A QQVSAVRT ...String: MVWSHPQFEK GGGSGGGSGG SAWSHPQFEK GDYPYDVPDY AGTENLYFQG LVDMKSPALQ PLSMAGLQLM TPASSPMGPF FGLPWQQEA IHDNIYTPRK YQVELLEAAL DHNTIVCLNT GSGKTFIAVL LTKELAHQIR GDLNPHAKRT VFLVNSANQV A QQVSAVRT HSDLKVGEYS DLEVNASWTK ERWSQEFTKH QVLIMTCYVA LTVLKNGYLS LSDINLLVFD ECHLAILDHP YR EIMKLCE SCPSCPRILG LTASILNGKC DPEELEEKIQ KLERILRSDA ETATDLVVLD RYTSQPCEIV VDCGPFTDRS GLY ERLLME LEAALDFIND CNVAVHSKER DSTLISKQIL SDCRAVLVVL GPWCADKVAG MMVRELQKYI KHEQEELHRK FLLF TDTLL RKIHALCEEY FSPASLDLKY VTPKVMKLLE ILRKYKPYER QQFESVEWYN NRNQDNYVSW SDSEDDDDDE EIEEK EKPE TNFPSPFTNI LCGIIFVERR YTAVVLNRLI KEAGKQDPEL AYISSNFITG HGIGKNQPRS KQMEAEFRKQ EEVLRK FRA HETNLLIATS VVEEGVDIPK CNLVVRFDLP TEYRSYVQSK GRARAPISNY VMLADTDKIK SFEEDLKTYK AIEKILR NK CSKSADGAEA DVHAGVDDED AFPPYVLRPD DGGPRVTINT AIGHINRYCA RLPSDPFTHL APKCRTRELP DGTFYSTL Y LPINSPLRAS IVGPPMDSVR LAERVVALIC CEKLHKIGEL DEHLMPVGKE TVKYEEELDL HDEEETSVPG RPGSTKRRQ CYPKAIPECL RESYPKPDQP CYLYVIGMVL TTPLPDELNF RRRKLYPPED TTRCFGILTA KPIPQIPHFP VYTRSGEVTI SIELKKSGF TLSQQMLELI TRLHQYIFSH ILRLEKPALE FKPTGAESAY CVLPLNVVND SGTLDIDFKF MEDIEKSEAR I GIPSTKYS KETPFVFKLE DYQDAVIIPR YRNFDQPHRF YVADVYTDLT PLSKFPSPEY ETFAEYYKTK YNLDLTNLNQ PL LDVDHTS SRLNLLTPRH LNQKGKALPL SSAEKRKAKW ESLQNKQILV PELCAIHPIP ASLWRKAVCL PSILYRLHCL LTA EELRAQ TASDAGVGVR SLPVDFRYPN LDFGWKKSID SKSFISSCNS SLAESDNYCK HSTTVVPEHA AHQGATRPSL ENHD QMSVN CKRLPAESPA KLQSEVSTDL TAINGLSYNK NLANGSYDLV NRDFCQGNQL NYFKQEIPVQ PTTSYPIQNL YNYEN QPKP SNECPLLSNT YLDGNANTST SDGSPAVSTM PAMMNAVKAL KDRMDSEQSP SVGYSSRTLG PNPGLILQAL TLSNAS DGF NLERLEMLGD SFLKHAITTY LFCTYPDAHE GRLSYMRSKK VSNCNLYRLG KKKGLPSRMV VSIFDPPVNW LPPGYVV NQ DKSNSEKWEK DEMTKDCLLA NGKLGEACEE EEDLTWRAPK EEAEDEDDFL EYDQEHIQFI DSMLMGSGAF VRKISLSP F SASDSAYEWK MPKKASLGSM PFASGLEDFD YSSWDAMCYL DPSKAVEEDD FVVGFWNPSE ENCGVDTGKQ SISYDLHTE QCIADKSIAD CVAALLGCYL TSCGERAAQL FLCSLGLKVL PVIKRTSREK ALDPAQENGS SQQKSLSGSC ASPVGPRSSA GKDLEYGCL KIPPRCMFDH PDAEKTLNHL ISGFETFEKK INYRFKNKAY LLQAFTHASY HYNTITDCYQ RLEFLGDAIL D YLITKHLY EDPRQHSPGV LTDLRSALVN NTIFASLAVK YDYHKYFKAV SPELFHVIDD FVKFQLEKNE MQGMDSELRR SE EDEEKEE DIEVPKAMGD IFASLAGAIY MDSGMSLEVV WQVYYPMMQP LIEKFSANVP RSPVRELLEM EPETAKFSPA ERT YDGKVR VTVEVVGKGK FKGVGRSYRI AKSAAARRAL RSLKANQPQV PNSGRGENLY FQGASDYKDH DGDYKDHDGS HHHH HHHH UniProtKB: Endoribonuclease Dicer |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.20 mg/mL | ||||||||||
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Buffer | pH: 8 Component:
Details: The buffer was always prepared fresh | ||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Described in STAR methods. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 6354 / Average electron dose: 55.0 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: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | Endoribonuclease mouse Dicer from AlphaFold database was used as initial model. Initial local fitting into combined map from locally refined protein parts was done using Chimera and then Coot's Real Space Refine Zone. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8 Target criteria: Ramachandran Plot, Rotamer Analysis, Density Analysis |
Output model | ![]() PDB-7yz4: |
-Atomic model buiding 2
Details | PHENIX Real-space refinement was used for flexible fitting. |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8 / Target criteria: Correlation coefficient |
Output model | ![]() PDB-7yz4: |
-Atomic model buiding 3
Details | ISOLDE was used for flexible fitting with defined torsion restraints |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 87.8 Target criteria: Ramachandran Plot, Rotamer Analysis, Clash Score |
Output model | ![]() PDB-7yz4: |