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

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Basic information

Entry
Database: PDB / ID: 4ngc
TitleStructure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having UA-3' ends (2.1 Angstrom resolution)
Components
  • 5'-R(*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*A)-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 / molecular replacement / Resolution: 2.104 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*A)-3'


Theoretical massNumber of molelcules
Total (without water)38,7412
Polymers38,7412
Non-polymers00
Water4,089227
1
B: 5'-R(*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*A)-3'

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


Theoretical massNumber of molelcules
Total (without water)42,5533
Polymers42,5533
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*A)-3'

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


Theoretical massNumber of molelcules
Total (without water)77,4814
Polymers77,4814
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3890 Å2
ΔGint-27 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.081, 84.482, 51.550
Angle α, β, γ (deg.)90.000, 113.490, 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*A)-3'


Mass: 3812.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M sodium/potassium tartrate, 0.1 M Bis-Tris propane, pH 7.0, 18-22% PEG3350, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2009
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23726 / % possible obs: 95.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.86 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.056 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.10.21418930.387175.8
2.18-2.263.90.19522180.424190
2.26-2.374.60.16823810.453195.7
2.37-2.495.10.14424020.475197.7
2.49-2.655.30.1224660.537198.4
2.65-2.855.30.09424390.694198.7
2.85-3.145.30.07724541.18198.7
3.14-3.595.30.06624751.843199.2
3.59-4.525.10.05424742.095199.2
4.52-505.10.04325241.7199.1

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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: 2.104→34.179 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8558 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1202 5.07 %RANDOM
Rwork0.1719 ---
obs0.1735 23700 95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.22 Å2 / Biso mean: 33.3809 Å2 / Biso min: 11.61 Å2
Refinement stepCycle: LAST / Resolution: 2.104→34.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 252 0 227 2716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082635
X-RAY DIFFRACTIONf_angle_d1.1213652
X-RAY DIFFRACTIONf_chiral_restr0.079425
X-RAY DIFFRACTIONf_plane_restr0.006416
X-RAY DIFFRACTIONf_dihedral_angle_d12.9791030
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.104-2.18870.25331070.19771973208075
2.1887-2.28830.26971180.18862392251091
2.2883-2.40890.23151390.1772515265496
2.4089-2.55980.2241230.18332600272398
2.5598-2.75740.2291300.18572599272999
2.7574-3.03470.2371420.18582579272199
3.0347-3.47350.19741440.17622594273899
3.4735-4.37480.17811450.14792616276199
4.3748-34.18320.1781540.16882630278498
Refinement TLS params.Method: refined / Origin x: 35.038 Å / Origin y: 55.468 Å / Origin z: 6.6969 Å
111213212223313233
T0.1234 Å20.0075 Å2-0.0013 Å2-0.1586 Å2-0.0113 Å2--0.1524 Å2
L0.7272 °20.0358 °2-0.1439 °2-1.2757 °2-0.6304 °2--1.3489 °2
S-0.0223 Å °-0.036 Å °0.0214 Å °-0.0009 Å °-0.0024 Å °-0.0396 Å °0.0046 Å °0.0535 Å °0.0122 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA755 - 1308
2X-RAY DIFFRACTION1allB1 - 119

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