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- PDB-3dfv: Adjacent GATA DNA binding -

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Basic information

Entry
Database: PDB / ID: 3dfv
TitleAdjacent GATA DNA binding
Components
  • DNA (5'-D(*DAP*DAP*DGP*DCP*DAP*DGP*DAP*DTP*DAP*DAP*DGP*DTP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DG)-3')
  • DNA (5'-D(*DTP*DTP*DCP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DAP*DCP*DTP*DTP*DAP*DTP*DCP*DTP*DGP*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 / ureter morphogenesis / : / regulation of cellular response to X-ray / : / : / type IV hypersensitivity / regulation of CD4-positive, alpha-beta T cell differentiation / ureteric bud formation / positive regulation of thyroid hormone generation ...nephric duct formation / ureter morphogenesis / : / regulation of cellular response to X-ray / : / : / type IV hypersensitivity / regulation of CD4-positive, alpha-beta T cell differentiation / ureteric bud formation / positive regulation of thyroid hormone generation / positive regulation of ureteric bud formation / HMG box domain binding / otic vesicle development / nephric duct morphogenesis / anatomical structure formation involved in morphogenesis / pro-T cell differentiation / immune system development / cellular response to interferon-alpha / cardiac right ventricle morphogenesis / ureter maturation / parathyroid gland development / interleukin-2 receptor binding / negative regulation of mammary gland epithelial cell proliferation / norepinephrine biosynthetic process / regulation of epithelial cell differentiation / regulation of nephron tubule epithelial cell differentiation / parathyroid hormone secretion / mast cell differentiation / positive regulation of transcription regulatory region DNA binding / positive regulation of signal transduction / mesonephros development / lymphocyte migration / 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 / Estrogen-dependent gene expression / sympathetic nervous system development / ear development / histone methyltransferase binding / pharyngeal system development / cell activation / positive regulation of interleukin-5 production / cellular response to BMP stimulus / positive regulation of interleukin-13 production / cell fate determination / Ub-specific processing proteases / embryonic hemopoiesis / negative regulation of cell motility / lens development in camera-type eye / thymic T cell selection / cartilage development / ventricular septum development / aortic valve morphogenesis / inner ear morphogenesis / T-helper 2 cell differentiation / positive regulation of T cell differentiation / negative regulation of interleukin-2 production / negative regulation of epithelial to mesenchymal transition / uterus development / regulation of establishment of cell polarity / regulation of neuron projection development / positive regulation of interleukin-4 production / cellular response to cytokine stimulus / E-box binding / negative regulation of type II interferon production / humoral immune response / negative regulation of cell cycle / macrophage differentiation / homeostasis of number of cells / T cell differentiation / TOR signaling / cochlea development / canonical Wnt signaling pathway / embryonic organ development / negative regulation of endothelial cell apoptotic process / cell fate commitment / developmental growth / cis-regulatory region sequence-specific DNA binding / cell maturation / cellular response to interleukin-4 / regulation of cytokine production / thymus development / positive regulation of endothelial cell migration / post-embryonic development / regulation of neuron apoptotic process / axon guidance / positive regulation of cytokine production / kidney development / erythrocyte differentiation / response to gamma radiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of cell differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / male gonad development / negative regulation of inflammatory response / positive regulation of miRNA transcription / response to estrogen / DNA-binding transcription repressor activity, RNA polymerase II-specific / neuron migration
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 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 1.3Oct 30, 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_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
Y: DNA (5'-D(*DTP*DTP*DCP*DTP*DGP*DAP*DTP*DAP*DAP*DGP*DAP*DCP*DTP*DTP*DAP*DTP*DCP*DTP*DGP*DC)-3')
Z: DNA (5'-D(*DAP*DAP*DGP*DCP*DAP*DGP*DAP*DTP*DAP*DAP*DGP*DTP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DG)-3')
D: Trans-acting T-cell-specific transcription factor GATA-3
C: Trans-acting T-cell-specific transcription factor GATA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4846
Polymers26,3534
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-40 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.977, 35.756, 54.487
Angle α, β, γ (deg.)90.000, 113.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 6098.963 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DAP*DGP*DCP*DAP*DGP*DAP*DTP*DAP*DAP*DGP*DTP*DCP*DTP*DTP*DAP*DTP*DCP*DAP*DG)-3')


Mass: 6166.030 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
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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 290 K / 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: 8.2.1 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 210 / 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: 3.1→30 Å / Num. obs: 4593 / % possible obs: 99.9 % / Rmerge(I) obs: 0.078 / Χ2: 1.742 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.210.1644370.927100
3.21-3.340.0784501.015100
3.34-3.490.0944641.186100
3.49-3.670.1044371.373100
3.67-3.90.1074771.556100
3.9-4.210.0984451.79899.6
4.21-4.630.0984602.419100
4.63-5.290.0884642.203100
5.29-6.660.0714662.489100
6.66-300.0444932.49399.2

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Phasing

PhasingMethod: molecular replacement

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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
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 400
RfactorNum. reflection% reflection
Rfree0.289 336 7.3 %
Rwork0.276 --
obs-4032 87.4 %
Solvent computationBsol: 19.348 Å2
Displacement parametersBiso max: 160.92 Å2 / Biso mean: 48.076 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--35.149 Å20 Å2-19.087 Å2
2--14.628 Å20 Å2
3---20.521 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 814 2 0 1800
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.7261.5
X-RAY DIFFRACTIONc_scbond_it3.0692
X-RAY DIFFRACTIONc_mcangle_it4.6792
X-RAY DIFFRACTIONc_scangle_it5.3522.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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