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

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Basic information

Entry
Database: PDB / ID: 4ngf
TitleStructure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 17-mer siRNA having 5'-p and UU-3' ends (3.1 Angstrom resolution)
Components
  • 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*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 / ribonuclease III / positive regulation of myelination / 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 / ribonuclease III / positive regulation of myelination / 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
RNA / RNA (> 10) / Endoribonuclease Dicer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.101 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_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Endoribonuclease Dicer
C: Endoribonuclease Dicer
D: Endoribonuclease Dicer
E: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'
F: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'
G: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'
H: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)161,6118
Polymers161,6118
Non-polymers00
Water0
1
A: Endoribonuclease Dicer
G: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'
H: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)45,7613
Polymers45,7613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoribonuclease Dicer
E: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'
F: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)45,7613
Polymers45,7613
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Endoribonuclease Dicer
D: Endoribonuclease Dicer
G: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'
H: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)80,8054
Polymers80,8054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-51 kcal/mol
Surface area34170 Å2
MethodPISA
4
B: Endoribonuclease Dicer
C: Endoribonuclease Dicer
E: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'
F: 5'-R(P*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)80,8054
Polymers80,8054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-49 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.245, 104.191, 368.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
12chain E
22chain F
32chain G
42chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNCYSCYSchain AAA756 - 10533 - 300
21GLNGLNCYSCYSchain BBB756 - 10533 - 300
31GLNGLNCYSCYSchain CCC756 - 10533 - 300
41GLNGLNCYSCYSchain DDD756 - 10533 - 300
12UUUUchain EEE1 - 171 - 17
22UUUUchain FFF1 - 171 - 17
32UUUUchain GGG1 - 171 - 17
42UUUUchain HHH1 - 171 - 17

NCS ensembles :
ID
1
2

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Components

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


Mass: 35044.543 Da / Num. of mol.: 4
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*UP*CP*GP*AP*AP*GP*GP*UP*CP*CP*UP*UP*CP*GP*UP*UP*U)-3'


Mass: 5358.166 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: siRNA

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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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.08 M HEPES sodium, pH 7.5, 8% 2-propanol, 16% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2011
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 32098 / % possible obs: 91.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 76.58 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.1-3.2113.40.65187.8
3.21-3.3413.40.507187.1
3.34-3.4913.40.402187
3.49-3.6813.30.297187.8
3.68-3.9113.30.212187.1
3.91-4.2113.10.168187.6
4.21-4.6312.60.134192.2
4.63-5.312.10.118198.9
5.3-6.6713.10.1031100
6.67-5013.50.056199.7

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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
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NGD

4ngd


Resolution: 3.101→42.478 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 28.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2703 1589 4.96 %
Rwork0.2231 --
obs0.2255 32027 91.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.9396 Å2
Refinement stepCycle: LAST / Resolution: 3.101→42.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8273 1428 0 0 9701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610081
X-RAY DIFFRACTIONf_angle_d1.16514052
X-RAY DIFFRACTIONf_dihedral_angle_d13.9833909
X-RAY DIFFRACTIONf_chiral_restr0.0481677
X-RAY DIFFRACTIONf_plane_restr0.0061527
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4835X-RAY DIFFRACTION17.495TORSIONAL
12B4835X-RAY DIFFRACTION17.495TORSIONAL
13C4835X-RAY DIFFRACTION17.495TORSIONAL
14D4835X-RAY DIFFRACTION17.495TORSIONAL
21E804X-RAY DIFFRACTION17.495TORSIONAL
22F804X-RAY DIFFRACTION17.495TORSIONAL
23G804X-RAY DIFFRACTION17.495TORSIONAL
24H804X-RAY DIFFRACTION17.495TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1008-3.20090.35081330.23982425X-RAY DIFFRACTION82
3.2009-3.31520.33661430.24992615X-RAY DIFFRACTION87
3.3152-3.44790.30481440.2472623X-RAY DIFFRACTION87
3.4479-3.60480.2851200.23162631X-RAY DIFFRACTION87
3.6048-3.79470.22651230.21592641X-RAY DIFFRACTION87
3.7947-4.03230.30511440.21542619X-RAY DIFFRACTION87
4.0323-4.34330.26991390.20792682X-RAY DIFFRACTION89
4.3433-4.77990.22071470.19382912X-RAY DIFFRACTION95
4.7799-5.47030.26821560.21233032X-RAY DIFFRACTION100
5.4703-6.88730.29381680.25343058X-RAY DIFFRACTION100
6.8873-42.48160.2521720.22473200X-RAY DIFFRACTION100

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