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

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Basic information

Entry
Database: PDB / ID: 4nha
TitleStructure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 16-mer siRNA having 5'-p and UU-3' ends (3.4 Angstrom resolution)
Components
  • 5'-R(P*GP*CP*GP*UP*UP*GP*GP*CP*CP*AP*AP*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 / pre-miRNA binding / global gene silencing by mRNA cleavage / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / apoptotic DNA fragmentation / tRNA decay / positive regulation of myelination / ribonuclease III ...peripheral nervous system myelin formation / pre-miRNA binding / global gene silencing by mRNA cleavage / Small interfering RNA (siRNA) biogenesis / negative regulation of Schwann cell proliferation / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / apoptotic DNA fragmentation / tRNA decay / positive regulation of myelination / ribonuclease III / deoxyribonuclease I activity / nerve development / positive regulation of Schwann cell differentiation / RISC-loading complex / miRNA metabolic process / RISC complex assembly / miRNA processing / ribonuclease III activity / pre-miRNA processing / siRNA processing / siRNA binding / Regulation of MITF-M-dependent genes involved in apoptosis / 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 / RNA binding / extracellular exosome / ATP binding / nucleus / metal ion binding / 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 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 / SAD / Resolution: 3.401 Å
AuthorsSimanshu, D.K. / Tian, Y. / Ma, J.-B. / 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 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Nov 20, 2024Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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*GP*CP*GP*UP*UP*GP*GP*CP*CP*AP*AP*CP*GP*CP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)40,3222
Polymers40,3222
Non-polymers00
Water00
1
B: 5'-R(P*GP*CP*GP*UP*UP*GP*GP*CP*CP*AP*AP*CP*GP*CP*UP*U)-3'

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


Theoretical massNumber of molelcules
Total (without water)45,4123
Polymers45,4123
Non-polymers00
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation15_555y,x,-z1
identity operation1_555x,y,z1
2
A: Endoribonuclease Dicer
B: 5'-R(P*GP*CP*GP*UP*UP*GP*GP*CP*CP*AP*AP*CP*GP*CP*UP*U)-3'

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


Theoretical massNumber of molelcules
Total (without water)80,6444
Polymers80,6444
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_555y,x,-z1
Buried area3320 Å2
ΔGint-17 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.469, 174.469, 74.757
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 35232.121 Da / Num. of mol.: 1
Fragment: platform-PAZ-connector helix cassette (UNP residues 765-1065)
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*GP*CP*GP*UP*UP*GP*GP*CP*CP*AP*AP*CP*GP*CP*UP*U)-3'


Mass: 5090.056 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: siRNA
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: 3.53 Å3/Da / Density % sol: 65.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M potassium chloride, 0.1 M magnesium acetate, 0.05 M sodium cacodylate, pH 6.5, 12 % 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: 0.97947 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Number: 55198 / Rmerge(I) obs: 0.063 / Χ2: 1.12 / D res high: 3.4 Å / D res low: 20 Å / Num. obs: 14941 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.222099.110.0341.6833.8
5.787.2299.510.0541.2543.7
5.065.7899.510.0661.2223.8
4.65.0699.710.0741.2443.8
4.284.699.810.0851.1883.8
4.034.2899.910.1151.0563.7
3.834.0399.810.1550.9723.6
3.663.8399.310.2120.9023.6
3.523.6698.210.2950.7933.5
3.43.5297.610.3550.8293.5
ReflectionResolution: 3.4→20 Å / Num. obs: 8091 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 107.44 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 30.4
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4.28 / Num. unique all: 769

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.401→19.752 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6862 / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3174 807 10 %RANDOM
Rwork0.2768 ---
obs0.2808 8068 98.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 298.01 Å2 / Biso mean: 142.7845 Å2 / Biso min: 69.11 Å2
Refinement stepCycle: LAST / Resolution: 3.401→19.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 340 0 0 2114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062196
X-RAY DIFFRACTIONf_angle_d1.1913078
X-RAY DIFFRACTIONf_chiral_restr0.086380
X-RAY DIFFRACTIONf_plane_restr0.005328
X-RAY DIFFRACTIONf_dihedral_angle_d14.17820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.401-3.61330.40571280.33441152128097
3.6133-3.89030.37381330.30831196132999
3.8903-4.27820.32511340.281412051339100
4.2782-4.88910.29671340.2531213134799
4.8891-6.1290.33021370.28781220135799
6.129-19.75250.28541410.2621275141698
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)
11.2696-1.7719-1.48193.57770.37564.65720.29432.5816-0.89020.1076-0.57120.5892-0.24890.02330.40971.0330.1861-0.20113.1681-0.15010.614-18.33373.6916-25.1738
25.704-6.4556.4547.7072-7.1077.3617-1.33922.82440.52391.96990.9128-0.2006-2.05610.73070.27550.9569-0.2270.08992.79330.34590.9733-14.667616.8506-18.1442
35.13542.52192.82521.67252.86246.54230.3172-0.430.10890.0397-2.1032-1.2358-1.0855-1.03631.28380.9141-0.0373-0.00641.22570.2381.7625-36.887521.90620.1499
42.5877-2.10512.07589.22951.09248.1145-0.1602-0.14920.10231.30210.01440.69230.6257-1.29260.06440.8615-0.13670.22241.2674-0.00370.8403-33.91657.68712.1139
55.55391.46911.22811.37690.12491.78120.86830.5141-1.2025-0.3221-0.05240.03710.30810.1753-0.89121.4859-0.042-0.73942.8305-0.17960.7592-14.555-6.1015-14.3476
68.8751-8.9599-3.328.80713.0991.2339-0.3529-1.0903-2.54780.84910.4361.49781.1644-0.6673-0.0521.6897-0.1252-0.25841.67880.43491.8133-19.8512-14.45822.5731
74.1291-0.1516-1.40783.54940.45664.7590.22021.36220.1569-0.3387-0.07420.49980.37571.74220.14090.2544-0.32650.29952.72770.27050.3913-21.50196.2432-11.7029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and ( resseq 760:829 )A760 - 829
2X-RAY DIFFRACTION2chain A and ( resseq 830:891 )A830 - 891
3X-RAY DIFFRACTION3chain A and ( resseq 892:913 )A892 - 913
4X-RAY DIFFRACTION4chain A and ( resseq 914:984 )A914 - 984
5X-RAY DIFFRACTION5chain A and ( resseq 985:992 )A985 - 992
6X-RAY DIFFRACTION6chain B and ( resseq 1:16 )B1 - 16
7X-RAY DIFFRACTION7chain A and ( resseq 1021:1053 )A1021 - 1053

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