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- PDB-3le4: Crystal structure of the DGCR8 dimerization domain -

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Basic information

Entry
Database: PDB / ID: 3le4
TitleCrystal structure of the DGCR8 dimerization domain
ComponentsMicroprocessor complex subunit DGCR8
KeywordsNUCLEAR PROTEIN / WW motif / dimerization / 3D domain swapping / heme binding / microRNA processing / Heme / Iron / Metal-binding / Nucleus / Phosphoprotein / RNA-binding
Function / homology
Function and homology information


positive regulation of pre-miRNA processing / protein-RNA adaptor activity / primary miRNA binding / Transcriptional Regulation by MECP2 / primary miRNA processing / regulation of stem cell proliferation / microprocessor complex / MicroRNA (miRNA) biogenesis / double-stranded RNA binding / protein-macromolecule adaptor activity ...positive regulation of pre-miRNA processing / protein-RNA adaptor activity / primary miRNA binding / Transcriptional Regulation by MECP2 / primary miRNA processing / regulation of stem cell proliferation / microprocessor complex / MicroRNA (miRNA) biogenesis / double-stranded RNA binding / protein-macromolecule adaptor activity / site of double-strand break / postsynaptic density / nuclear body / glutamatergic synapse / DNA damage response / heme binding / nucleolus / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Microprocessor complex subunit DGCR8 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...Microprocessor complex subunit DGCR8 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Ubiquitin Ligase Nedd4; Chain: W; / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Microprocessor complex subunit DGCR8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.701 Å
AuthorsSenturia, R. / Cascio, D. / Sawaya, M. / Guo, F.
CitationJournal: Protein Sci. / Year: 2010
Title: Structure of the dimerization domain of DiGeorge Critical Region 8
Authors: Senturia, R. / Faller, M. / Yin, S. / Loo, J.A. / Cascio, D. / Sawaya, M.R. / Hwang, D. / Clubb, R.T. / Guo, F.
History
DepositionJan 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microprocessor complex subunit DGCR8


Theoretical massNumber of molelcules
Total (without water)8,8881
Polymers8,8881
Non-polymers00
Water64936
1
A: Microprocessor complex subunit DGCR8

A: Microprocessor complex subunit DGCR8


Theoretical massNumber of molelcules
Total (without water)17,7772
Polymers17,7772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2600 Å2
ΔGint-17 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.952, 39.952, 80.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Microprocessor complex subunit DGCR8 / DiGeorge syndrome critical region 8


Mass: 8888.265 Da / Num. of mol.: 1 / Fragment: Dimerization domain (UNP residues 275 to 353)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DGCR8, C22orf12, DGCRK6, LP4941 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WYQ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.81 Å3/Da / Density % sol: 32.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium acetate, 100 mM Bis-Tris pH 5.5, 25% polyethylene glycol 3350, 10 mM nicotinamide adenine dinucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Mar 29, 2009
RadiationMonochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→28.3 Å / Num. all: 7721 / Num. obs: 7721 / % possible obs: 99.9 %
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.701→28.25 Å / SU ML: 0.14 / σ(F): 0.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 347 4.67 %Random
Rwork0.1808 ---
obs0.1823 7721 96.85 %-
all-7721 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.549 Å2 / ksol: 0.43 e/Å3
Refinement stepCycle: LAST / Resolution: 1.701→28.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms440 0 0 36 476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009475
X-RAY DIFFRACTIONf_angle_d1.327652
X-RAY DIFFRACTIONf_dihedral_angle_d13.981174
X-RAY DIFFRACTIONf_chiral_restr0.08368
X-RAY DIFFRACTIONf_plane_restr0.00684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7014-1.760.19891490.16673389X-RAY DIFFRACTION95
2.1435-28.25420.21711980.18553699X-RAY DIFFRACTION99

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