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- PDB-3dfx: Opposite GATA DNA binding -

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Basic information

Entry
Database: PDB / ID: 3dfx
TitleOpposite GATA DNA binding
Components
  • DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3')
  • DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3')
  • Trans-acting T-cell-specific transcription factor GATA-3
KeywordsTranscription/DNA / Activator / DNA-binding / Metal-binding / Nucleus / Transcription / Transcription regulation / Zinc / Zinc-finger / Transcription-DNA COMPLEX
Function / homology
Function and homology information


nephric duct formation / : / regulation of cellular response to X-ray / : / : / type IV hypersensitivity / regulation of CD4-positive, alpha-beta T cell differentiation / ureter morphogenesis / thymic T cell selection / ureteric bud formation ...nephric duct formation / : / regulation of cellular response to X-ray / : / : / type IV hypersensitivity / regulation of CD4-positive, alpha-beta T cell differentiation / ureter morphogenesis / thymic T cell selection / ureteric bud formation / positive regulation of thyroid hormone generation / positive regulation of ureteric bud formation / HMG box domain binding / otic vesicle development / anatomical structure formation involved in morphogenesis / nephric duct morphogenesis / immune system development / pro-T cell differentiation / interleukin-2 receptor binding / cardiac right ventricle morphogenesis / parathyroid gland development / negative regulation of mammary gland epithelial cell proliferation / ureter maturation / norepinephrine biosynthetic process / regulation of nephron tubule epithelial cell differentiation / parathyroid hormone secretion / cellular response to interferon-alpha / mast cell differentiation / regulation of epithelial cell differentiation / positive regulation of transcription regulatory region DNA binding / positive regulation of signal transduction / lymphocyte migration / mesonephros development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of T-helper 2 cell cytokine production / mesenchymal to epithelial transition / Factors involved in megakaryocyte development and platelet production / ear development / Estrogen-dependent gene expression / histone methyltransferase binding / cell activation / pharyngeal system development / sympathetic nervous system development / positive regulation of interleukin-5 production / positive regulation of interleukin-13 production / cellular response to BMP stimulus / cell fate determination / Ub-specific processing proteases / negative regulation of cell motility / cartilage development / lens development in camera-type eye / aortic valve morphogenesis / embryonic hemopoiesis / T-helper 2 cell differentiation / negative regulation of epithelial to mesenchymal transition / ventricular septum development / negative regulation of interleukin-2 production / inner ear morphogenesis / positive regulation of T cell differentiation / regulation of establishment of cell polarity / regulation of neuron projection development / positive regulation of interleukin-4 production / cellular response to cytokine stimulus / uterus development / E-box binding / negative regulation of cell cycle / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / TOR signaling / T cell differentiation / homeostasis of number of cells / cochlea development / developmental growth / cell fate commitment / canonical Wnt signaling pathway / embryonic organ development / negative regulation of endothelial cell apoptotic process / cis-regulatory region sequence-specific DNA binding / cell maturation / positive regulation of endothelial cell migration / regulation of cytokine production / cellular response to interleukin-4 / axon guidance / regulation of neuron apoptotic process / thymus development / positive regulation of cytokine production / response to gamma radiation / erythrocyte differentiation / post-embryonic development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell differentiation / kidney development / positive regulation of miRNA transcription / negative regulation of inflammatory response / response to estrogen / DNA-binding transcription repressor activity, RNA polymerase II-specific / male gonad development / transcription coactivator binding
Similarity search - Function
Transcription factor, GATA-2/3 / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type ...Transcription factor, GATA-2/3 / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Trans-acting T-cell-specific transcription factor GATA-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsBates, D.L. / Kim, G.K. / Guo, L. / Chen, L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA.
Authors: Bates, D.L. / Chen, Y. / Kim, G. / Guo, L. / Chen, L.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
X: DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3')
Y: DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3')
A: Trans-acting T-cell-specific transcription factor GATA-3
B: Trans-acting T-cell-specific transcription factor GATA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4836
Polymers26,3524
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-36 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.882, 30.370, 75.648
Angle α, β, γ (deg.)90.000, 93.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3')


Mass: 6150.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3')


Mass: 6113.975 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Trans-acting T-cell-specific transcription factor GATA-3 / GATA-binding factor 3


Mass: 7044.058 Da / Num. of mol.: 2 / Fragment: UNP residues 308-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gata3, Gata-3 / Plasmid: pEt28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plyS / References: UniProt: P23772
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 290 K / Method: hanging drop / pH: 6.5
Details: 20 mM Mg(OAc), Cacodylic acid, 30% PEG 4K , pH 6.5, hanging drop, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Cacodylic acid11
2Mg(OAc)11
3Cacodylic acid12
4Mg(OAc)12
5PEG 4K12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 8491 / % possible obs: 99.9 % / Rmerge(I) obs: 0.085 / Χ2: 1.951 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.80.4528271.077100
2.8-2.910.3288311.157100
2.91-3.040.2518721.295100
3.04-3.20.1428021.538100
3.2-3.40.1018561.89499.9
3.4-3.660.0878182.161100
3.66-4.030.0748582.414100
4.03-4.610.0688562.628100
4.61-5.80.0678672.801100
5.8-300.0489042.63699.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.7→25.32 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.755
RfactorNum. reflection
Rfree0.298 864
Rwork0.276 -
obs-8145
Displacement parametersBiso max: 170.54 Å2 / Biso mean: 61.468 Å2 / Biso min: 7.47 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 814 2 0 1710

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