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- PDB-7yz4: Mouse endoribonuclease Dicer (composite structure) -

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Basic information

Entry
Database: PDB / ID: 7yz4
TitleMouse endoribonuclease Dicer (composite structure)
ComponentsEndoribonuclease Dicer
KeywordsRNA BINDING PROTEIN / endoribonuclease / gene silencing / post-transcriptional / catalytic enzyme / cytoplasm
Function / homology
Function and homology information


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 RNA metabolic process ...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 RNA metabolic process / trophectodermal cell proliferation / regulation of odontogenesis of dentin-containing tooth / regulation of enamel mineralization / regulation of miRNA metabolic process / spermatogonial cell division / peripheral nervous system myelin formation / regulation of epithelial cell differentiation / regulation of regulatory T cell differentiation / global gene silencing by mRNA cleavage / spinal cord motor neuron differentiation / negative regulation of Schwann cell proliferation / epidermis morphogenesis / reproductive structure development / positive regulation of myelination / regulation of Notch signaling pathway / ribonuclease III / myoblast differentiation involved in skeletal muscle regeneration / nerve development / positive regulation of Schwann cell differentiation / inner ear receptor cell development / meiotic spindle organization / RISC-loading complex / regulatory ncRNA-mediated post-transcriptional gene silencing / RISC complex assembly / intestinal epithelial cell development / miRNA processing / ribonuclease III activity / pre-miRNA processing / siRNA processing / pericentric heterochromatin formation / regulation of stem cell differentiation / regulation of viral genome replication / RISC complex / mRNA stabilization / digestive tract development / embryonic limb morphogenesis / embryonic hindlimb morphogenesis / cardiac muscle cell development / miRNA binding / positive regulation of miRNA metabolic process / cartilage development / regulation of neuron differentiation / regulation of myelination / negative regulation of glial cell proliferation / hair follicle morphogenesis / branching morphogenesis of an epithelial tube / stem cell population maintenance / regulation of neurogenesis / hair follicle development / postsynaptic density, intracellular component / RNA processing / spindle assembly / spleen development / neuron projection morphogenesis / post-embryonic development / helicase activity / lung development / multicellular organism growth / cerebral cortex development / rRNA processing / regulation of gene expression / regulation of inflammatory response / gene expression / angiogenesis / defense response to virus / 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
Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Dicer, double-stranded RNA-binding domain / : / Dicer, partner-binding domain / Dicer, dsRNA-binding domain / Ribonuclease III / : / Dicer, platform domain / Dicer dimerisation domain ...Ribonuclease III domain / Ribonuclease iii, N-terminal Endonuclease Domain; Chain A / Dicer, double-stranded RNA-binding domain / : / Dicer, partner-binding domain / Dicer, dsRNA-binding domain / Ribonuclease III / : / 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 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Double-stranded RNA binding motif / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Endoribonuclease Dicer
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsZanova, M. / Zapletal, D. / Kubicek, K. / Stefl, R. / Pinkas, M. / Novacek, J.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science FoundationGA22-19896S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLM2018127 Czech Republic
CitationJournal: Mol Cell / Year: 2022
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
DepositionFeb 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoribonuclease Dicer


Theoretical massNumber of molelcules
Total (without water)226,8101
Polymers226,8101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area63990 Å2

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Components

#1: Protein Endoribonuclease Dicer / Double-strand-specific ribonuclease mDCR-1


Mass: 226809.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dicer1, Dicer, Mdcr / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q8R418, ribonuclease III

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Free form of mouse somatic dicer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 8 / Details: The buffer was always prepared fresh
Buffer component
IDConc.NameBuffer-ID
150 mMTris1
2100 mMSodium Chloride1
31 mMDithiotreitol1
42 mMMagensium Chloride1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Described in STAR methods

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6354

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetailsFitting-ID
5cryoSPARCv3.3.1CTF correction
8UCSF Chimera1.15model fittingFit to Map1
12cryoSPARCv3.3.1classification
14cryoSPARCv3.3.13D reconstruction
16Coot0.9.6model refinementReal Space Refine Zone1
32PHENIX1.19.2-4158model refinementReal-space refinement2
48ISOLDE1.1.0model refinement3
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 862842
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92906 / Algorithm: FOURIER SPACE
Details: The map resolution was further improved up to 3.47 with local refinement of the individual protein domains.
Num. of class averages: 81 / Symmetry type: POINT
Atomic model building
IDB valueProtocolSpaceTarget criteriaDetails
187.8FLEXIBLE FITREALRamachandran Plot, Rotamer Analysis, Density AnalysisEndoribonuclease 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.
287.8FLEXIBLE FITREALCorrelation coefficientPHENIX Real-space refinement was used for flexible fitting.
387.8FLEXIBLE FITREALRamachandran Plot, Rotamer Analysis, Clash ScoreISOLDE was used for flexible fitting with defined torsion restraints
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410066
ELECTRON MICROSCOPYf_angle_d0.77813634
ELECTRON MICROSCOPYf_dihedral_angle_d11.9463798
ELECTRON MICROSCOPYf_chiral_restr0.0461552
ELECTRON MICROSCOPYf_plane_restr0.0091732

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