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- PDB-3c4b: Structure of RNaseIIIb and dsRNA binding domains of mouse Dicer -

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Basic information

Entry
Database: PDB / ID: 3c4b
TitleStructure of RNaseIIIb and dsRNA binding domains of mouse Dicer
ComponentsEndoribonuclease Dicer
KeywordsHYDROLASE / RNase / dsRNA binding protein / ATP-binding / Endonuclease / Helicase / Nuclease / Nucleotide-binding / Phosphoprotein / RNA-binding / RNA-mediated gene silencing
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 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 RNA metabolic process / spermatogonial cell division / regulation of epithelial cell differentiation / 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 / inner ear receptor cell development / mRNA stabilization / 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
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 / Double Stranded RNA Binding Domain - #20 / 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 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Endoribonuclease Dicer
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.68 Å
AuthorsLee, J.K. / Du, Z. / Tjhen, R.J. / Stroud, R.M. / James, T.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural and biochemical insights into the dicing mechanism of mouse Dicer: A conserved lysine is critical for dsRNA cleavage.
Authors: Du, Z. / Lee, J.K. / Tjhen, R. / Stroud, R.M. / James, T.L.
History
DepositionJan 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoribonuclease Dicer


Theoretical massNumber of molelcules
Total (without water)30,9721
Polymers30,9721
Non-polymers00
Water5,531307
1
A: Endoribonuclease Dicer

A: Endoribonuclease Dicer


Theoretical massNumber of molelcules
Total (without water)61,9442
Polymers61,9442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area3300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.496, 66.496, 134.081
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-255-

HOH

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Components

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


Mass: 30971.912 Da / Num. of mol.: 1
Fragment: RNaseIII domain, dsRNA binding domain (UNP residues 1638-1900)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: mouse / Gene: Dicer1, Dicer, Mdcr / Plasmid: pet48b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(DE3)
References: UniProt: Q8R418, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20-26% PEG400, 100 mM HEPES pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.9795
SYNCHROTRONALS 8.2.220.9795
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDFeb 15, 2007KOHZU: Double Crystal Si(111)
ADSC QUANTUM 3152CCDFeb 15, 2007KOHZU: Double Crystal Si(111)
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.66→40 Å / Num. obs: 30584 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Biso Wilson estimate: 24.89 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.045 / Net I/σ(I): 31.7
Reflection shellResolution: 1.68→1.724 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.27 / Num. unique all: 1374 / Rsym value: 0.368 / % possible all: 56.55

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 1.68→40 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.43 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21036 1675 5.1 %RANDOM
Rwork0.17979 ---
obs0.1814 31447 94.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.111 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.104 Å0.106 Å
Refinement stepCycle: LAST / Resolution: 1.68→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 0 307 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222121
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9622876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1065265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94923.173104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38915390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7871517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211619
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8361.51261
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53222047
X-RAY DIFFRACTIONr_scbond_it2.7823860
X-RAY DIFFRACTIONr_scangle_it4.4044.5820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 67 -
Rwork0.243 1374 -
obs--56.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27980.1420.12190.49130.17250.4149-0.04050.0082-0.0165-0.08660.026-0.0227-0.06410.04110.01450.0165-0.01410.0065-0.00980.0045-0.050548.58724.55552.066
20.0496-0.0036-0.02680.3640.31850.9478-0.0528-0.0336-0.0276-0.03970.0693-0.03-0.04920.1342-0.0166-0.0041-0.01080.00650.0201-0.0049-0.038954.52825.17560.264
32.65190.7713-0.98020.4924-0.2260.7024-0.103-0.05720.1246-0.1110.02640.0662-0.00660.01370.0766-0.0086-0.018-0.0171-0.0016-0.0273-0.036959.3642.59690.208
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1646 - 176011 - 125
2X-RAY DIFFRACTION2AA1791 - 1838156 - 203
3X-RAY DIFFRACTION3AA1840 - 1900205 - 265

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