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- PDB-3c4t: Structure of RNaseIIIb and dsRNA binding domains of mouse Dicer -

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Basic information

Entry
Database: PDB / ID: 3c4t
TitleStructure of RNaseIIIb and dsRNA binding domains of mouse Dicer
ComponentsEndoribonuclease Dicer
KeywordsHYDROLASE / RNase / 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 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 / 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: 2.8 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 30, 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_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoribonuclease Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9344
Polymers30,5971
Non-polymers3373
Water1086
1
A: Endoribonuclease Dicer
hetero molecules

A: Endoribonuclease Dicer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8688
Polymers61,1942
Non-polymers6746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.126, 70.126, 132.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 30596.756 Da / Num. of mol.: 1
Fragment: RNaseIIIb domain, dsRNA binding domain (UNP residues 1638-1900)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house 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: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20-26% PEG400, 100 mM HEPES (pH7.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 5, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. all: 9091 / Num. obs: 7819 / % possible obs: 86 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 105 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.036 / Net I/σ(I): 28.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 3.67 / Num. unique all: 399 / Rsym value: 0.223 / % possible all: 46

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.915 / SU B: 43.196 / SU ML: 0.382 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30429 353 4.5 %RANDOM
Rwork0.23271 ---
obs0.23568 7513 90.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.858 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å20 Å20 Å2
2--6.44 Å20 Å2
3----12.88 Å2
Refine analyzeLuzzati coordinate error free: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1923 0 3 6 1932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221972
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1631.9552673
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9525240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.46623.15292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.87715324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8631513
X-RAY DIFFRACTIONr_chiral_restr0.1410.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211503
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_it0.7851.51207
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51521937
X-RAY DIFFRACTIONr_scbond_it2.093765
X-RAY DIFFRACTIONr_scangle_it3.5644.5736
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 18 -
Rwork0.469 292 -
obs--51.67 %
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)
10.8667-0.6143-0.34073.70151.36559.23260.26190.02320.02720.1319-0.1520.00150.2863-0.7121-0.1099-0.1057-0.2222-0.0759-0.06970.0624-0.1858-20.0051-25.400615.2561
22.1351.14950.27730.62250.32918.965-0.043-0.01710.36750.3880.4968-0.13150.77560.3882-0.45380.0163-0.0971-0.06-0.00580.0157-0.0407-13.6141-26.40787.1069
39.11010.21954.91436.99120.79329.39220.2923-0.11020.2135-0.2926-0.6586-1.0079-0.38330.41280.36630.0106-0.05760.1415-0.1365-0.0215-0.1656-9.2202-43.8798-23.528
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 - 1895205 - 260

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