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- PDB-4nh6: Structure of human Dicer Platform-PAZ-Connector Helix cassette in... -

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Basic information

Entry
Database: PDB / ID: 4nh6
TitleStructure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 15-mer siRNA having 5'-pUUU and UU-3' ends (2.55 Angstrom resolution)
Components
  • 5'-R(P*UP*UP*UP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
  • Endoribonuclease Dicer
KeywordsHYDROLASE/RNA / PAZ domain / platform domain / connector helix / siRNA / RNase III domain / endoribonuclease / pre-miRNA / HYDROLASE-RNA complex
Function / homology
Function and homology information


peripheral nervous system myelin formation / global gene silencing by mRNA cleavage / pre-miRNA binding / negative regulation of Schwann cell proliferation / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / Small interfering RNA (siRNA) biogenesis / apoptotic DNA fragmentation / tRNA decay / ribonuclease III / deoxyribonuclease I activity ...peripheral nervous system myelin formation / global gene silencing by mRNA cleavage / pre-miRNA binding / negative regulation of Schwann cell proliferation / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / Small interfering RNA (siRNA) biogenesis / apoptotic DNA fragmentation / tRNA decay / ribonuclease III / deoxyribonuclease I activity / positive regulation of Schwann cell differentiation / nerve development / 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 / paz domain / paz domain / : / Dicer, platform domain / Dicer dimerisation domain / Dicer dimerisation domain superfamily ...Dicer, double-stranded RNA-binding domain / : / Dicer, partner-binding domain / Dicer, dsRNA-binding domain / paz domain / paz 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 / Beta Complex / 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 / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Endoribonuclease Dicer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.551 Å
AuthorsSimanshu, D.K. / Tian, Y. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2014
Title: A Phosphate-Binding Pocket within the Platform-PAZ-Connector Helix Cassette of Human Dicer.
Authors: Tian, Y. / Simanshu, D.K. / Ma, J.B. / Park, J.E. / Heo, I. / Kim, V.N. / Patel, D.J.
History
DepositionNov 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: 5'-R(P*UP*UP*UP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)39,6362
Polymers39,6362
Non-polymers00
Water30617
1
B: 5'-R(P*UP*UP*UP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'

A: Endoribonuclease Dicer
B: 5'-R(P*UP*UP*UP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)44,3443
Polymers44,3443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_555-x,y,-z1
identity operation1_555x,y,z1
2
A: Endoribonuclease Dicer
B: 5'-R(P*UP*UP*UP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'

A: Endoribonuclease Dicer
B: 5'-R(P*UP*UP*UP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)79,2724
Polymers79,2724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5080 Å2
ΔGint-45 kcal/mol
Surface area32350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.036, 84.126, 51.496
Angle α, β, γ (deg.)90.00, 109.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Endoribonuclease Dicer / Helicase with RNase motif / Helicase MOI


Mass: 34928.336 Da / Num. of mol.: 1
Fragment: platform-PAZ-connector helix cassette (UNP residues 765-1065)
Mutation: K822A/K823A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DICER, DICER1, HERNA, KIAA0928 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9UPY3, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain 5'-R(P*UP*UP*UP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'


Mass: 4707.777 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium chloride, 0.05 M Tris-HCl, pH 8.3-8.8, 12-15% PEG20000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2010
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 15309 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 56.26 Å2 / Rmerge(I) obs: 0.073 / Χ2: 1.855 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.55-2.643.90.44914760.904196.7
2.64-2.754.10.35415150.903199.7
2.75-2.874.20.28615431.0661100
2.87-3.024.10.20415341.3091100
3.02-3.214.10.14615281.6381100
3.21-3.4640.11315341.9471100
3.46-3.8140.08515452.5181100
3.81-4.363.90.07115232.951199.9
4.36-5.493.80.05815513.012199.8
5.49-503.90.04215602.436198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NGD

4ngd


Resolution: 2.551→33.666 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM work R set: 0.678 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 36.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 766 5.01 %RANDOM
Rwork0.1932 ---
obs0.196 15281 99.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.48 Å2 / Biso mean: 84.1671 Å2 / Biso min: 38.19 Å2
Refinement stepCycle: LAST / Resolution: 2.551→33.666 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 307 0 17 2520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072605
X-RAY DIFFRACTIONf_angle_d1.0893620
X-RAY DIFFRACTIONf_chiral_restr0.069430
X-RAY DIFFRACTIONf_plane_restr0.005405
X-RAY DIFFRACTIONf_dihedral_angle_d14.2891017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.551-2.74790.43741480.30932815296397
2.7479-3.02430.36951460.256229313077100
3.0243-3.46160.27531460.223729193065100
3.4616-4.35970.24291470.174429113058100
4.3597-33.66870.19321790.16292939311899
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)
11.27720.2114-0.74573.0299-0.83224.0916-0.0949-0.1377-0.03390.0749-0.0008-0.04440.43870.20640.11160.45830.06740.08010.4422-0.01760.4934-22.885914.59056.8344
25.03081.0725-4.58170.242-0.96794.1765-0.2864-0.0454-0.66320.1472-0.0738-0.4047-0.55830.25560.3341.15-0.00820.30780.92020.01061.1737-1.1854-5.28842.0621
30.3657-0.0130.17970.524-0.39690.9438-0.0855-0.00020.0251-0.02910.0019-0.029-0.01360.34420.01180.38020.1322-0.25830.6232-0.06560.389-24.693512.94957.4024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 755:1052)A755 - 1052
2X-RAY DIFFRACTION2(chain B and resid 1:15)B1 - 15
3X-RAY DIFFRACTION3(chain A and resid 1101:1116 or chain B and resid 101:101)A1101 - 1116
4X-RAY DIFFRACTION3(chain A and resid 1101:1116 or chain B and resid 101:101)B101

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