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

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Basic information

Entry
Database: PDB / ID: 4ngg
TitleStructure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 13-mer siRNA having 5'-A and UU-3' ends (2.6 Angstrom resolution)
Components
  • 5'-R(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
  • Endoribonuclease DicerDicer
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 / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage / tRNA decay / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / positive regulation of myelination / ribonuclease III / deoxyribonuclease I activity ...peripheral nervous system myelin formation / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / global gene silencing by mRNA cleavage / tRNA decay / pre-miRNA binding / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / positive regulation of myelination / ribonuclease III / deoxyribonuclease I activity / apoptotic DNA fragmentation / miRNA metabolic process / nerve development / RISC-loading complex / positive regulation of Schwann cell differentiation / RISC complex assembly / miRNA processing / pre-miRNA processing / ribonuclease III activity / siRNA processing / siRNA binding / M-decay: degradation of maternal mRNAs by maternally stored factors / RISC complex / MicroRNA (miRNA) biogenesis / negative regulation of tumor necrosis factor production / negative regulation of tumor necrosis factor-mediated signaling pathway / RNA endonuclease activity / neuron projection morphogenesis / 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 / DNA binding / RNA binding / extracellular exosome / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
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 ...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 / Dicer dimerisation domain superfamily / 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 / PAZ domain profile. / 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 / 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
PHOSPHATE ION / RNA / RNA (> 10) / Endoribonuclease Dicer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: 5'-R(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1423
Polymers39,0472
Non-polymers951
Water37821
1
B: 5'-R(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'

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


Theoretical massNumber of molelcules
Total (without water)43,2604
Polymers43,1653
Non-polymers951
Water181
TypeNameSymmetry operationNumber
crystal symmetry operation4_565x,-y+1,-z1
identity operation1_555x,y,z1
2
A: Endoribonuclease Dicer
B: 5'-R(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)78,2846
Polymers78,0944
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3500 Å2
ΔGint-34 kcal/mol
Surface area33660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.897, 97.240, 106.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Endoribonuclease Dicer / 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(*AP*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3'


Mass: 4118.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.2 M sodium chloride, 0.1 M sodium/potassium phosphate, pH 6.0-6.4, 10% PEG8000, 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: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 16, 2009
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14296 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.269 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.6990.72214000.5861100
2.69-2.89.80.56714190.6231100
2.8-2.93100.39413880.6591100
2.93-3.08100.25514180.7321100
3.08-3.28100.17114210.8981100
3.28-3.53100.12314301.1341100
3.53-3.889.90.0914071.5661100
3.88-4.459.80.0714492.1081100
4.45-5.69.50.06114512.4561100
5.6-508.90.03615131.902199.3

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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: 2.6→33.421 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8016 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 711 5.05 %RANDOM
Rwork0.186 ---
obs0.1888 14068 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.34 Å2 / Biso mean: 54.6717 Å2 / Biso min: 22.87 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 270 5 21 2453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082521
X-RAY DIFFRACTIONf_angle_d1.0943497
X-RAY DIFFRACTIONf_chiral_restr0.067411
X-RAY DIFFRACTIONf_plane_restr0.005394
X-RAY DIFFRACTIONf_dihedral_angle_d13.633969
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6-2.80070.33291200.238426472767
2.8007-3.08230.29411560.230726102766
3.0823-3.52790.26481500.201526432793
3.5279-4.44320.22231490.167926712820
4.4432-33.42340.21041360.170527862922
Refinement TLS params.Method: refined / Origin x: -7.6471 Å / Origin y: 27.2647 Å / Origin z: 14.7966 Å
111213212223313233
T0.3411 Å20.0123 Å2-0.0316 Å2-0.3231 Å2-0.0111 Å2--0.3388 Å2
L2.234 °20.3653 °20.0908 °2-1.9375 °20.4346 °2--1.069 °2
S-0.1068 Å °0.0793 Å °0.3993 Å °-0.1023 Å °-0.0421 Å °0.3757 Å °-0.1206 Å °-0.0678 Å °0.114 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA756 - 1221
2X-RAY DIFFRACTION1allB1 - 13

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