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

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Basic information

Entry
Database: PDB / ID: 4ngb
TitleStructure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having UU-3' ends (2.25 Angstrom resolution)
Components
  • 5'-R(*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 / ribonuclease III activity / miRNA processing / 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 / Resolution: 2.25 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 1, 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(*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)38,7182
Polymers38,7182
Non-polymers00
Water3,495194
1
B: 5'-R(*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'

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


Theoretical massNumber of molelcules
Total (without water)42,5073
Polymers42,5073
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,y,-z1
identity operation1_555x,y,z1
2
A: Endoribonuclease Dicer
B: 5'-R(*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'

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


Theoretical massNumber of molelcules
Total (without water)77,4354
Polymers77,4354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3810 Å2
ΔGint-32 kcal/mol
Surface area32220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.455, 84.680, 51.634
Angle α, β, γ (deg.)90.000, 113.300, 90.000
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(*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'


Mass: 3789.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.8 M sodium/potassium tartrate, 0.1 M sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2008
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 20573 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 34.94 Å2 / Rmerge(I) obs: 0.099 / Χ2: 2.25 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.336.70.40420426.9511100
2.33-2.426.80.20820411.3131100
2.42-2.536.90.18120591.4131100
2.53-2.6770.16720751.5741100
2.67-2.836.90.14720311.861100
2.83-3.0570.12320522.0511100
3.05-3.3670.10920572.0491100
3.36-3.856.90.10320881.9591100
3.85-4.856.90.0920521.787199.9
4.85-506.70.0620761.708197.9

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Processing

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

4ngd


Resolution: 2.25→31.995 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8204 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 24.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 1056 5.14 %RANDOM
Rwork0.1824 ---
obs0.1844 20529 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.4 Å2 / Biso mean: 38.6897 Å2 / Biso min: 14.11 Å2
Refinement stepCycle: LAST / Resolution: 2.25→31.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2227 250 0 194 2671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092574
X-RAY DIFFRACTIONf_angle_d1.1313563
X-RAY DIFFRACTIONf_chiral_restr0.074419
X-RAY DIFFRACTIONf_plane_restr0.005406
X-RAY DIFFRACTIONf_dihedral_angle_d12.641995
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.35240.29251440.24432389253399
2.3524-2.47640.28371350.200424282563100
2.4764-2.63150.21751160.202724092525100
2.6315-2.83460.28311440.207324472591100
2.8346-3.11960.26871070.224512558100
3.1196-3.57050.22041180.187724502568100
3.5705-4.49650.18141430.15224562599100
4.4965-31.99810.19271490.17042443259298
Refinement TLS params.Method: refined / Origin x: 35.0907 Å / Origin y: 55.5212 Å / Origin z: 6.642 Å
111213212223313233
T0.1589 Å20.0087 Å2-0.003 Å2-0.1659 Å2-0.0025 Å2--0.1631 Å2
L0.2685 °20.0317 °2-0.1845 °2-0.3168 °2-0.1532 °2--0.4736 °2
S-0.0273 Å °-0.0321 Å °0.0071 Å °-0.0089 Å °0.0079 Å °0.0239 Å °0.0188 Å °0.0184 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA756 - 1284
2X-RAY DIFFRACTION1allB1 - 110

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