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- PDB-4hc7: Crystal structure of the full DNA binding domain of GATA3-complex 2 -

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Basic information

Entry
Database: PDB / ID: 4hc7
TitleCrystal structure of the full DNA binding domain of GATA3-complex 2
Components
  • DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')
  • DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
  • Trans-acting T-cell-specific transcription factor GATA-3
KeywordsTranscription/DNA / GATA transcription factor / zinc finger / Transcription-DNA complex
Function / homology
Function and homology information


nephric duct formation / negative regulation of cell proliferation involved in mesonephros development / regulation of cellular response to X-ray / negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation / negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation / ureter morphogenesis / thymic T cell selection / ureteric bud formation / positive regulation of ureteric bud formation / HMG box domain binding ...nephric duct formation / negative regulation of cell proliferation involved in mesonephros development / regulation of cellular response to X-ray / negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation / negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation / ureter morphogenesis / thymic T cell selection / ureteric bud formation / positive regulation of ureteric bud formation / HMG box domain binding / positive regulation of thyroid hormone generation / otic vesicle development / negative regulation of mammary gland epithelial cell proliferation / nephric duct morphogenesis / anatomical structure formation involved in morphogenesis / pro-T cell differentiation / cellular response to interferon-alpha / norepinephrine biosynthetic process / immune system development / interleukin-2 receptor binding / cardiac right ventricle morphogenesis / parathyroid gland development / ureter maturation / mesenchymal to epithelial transition / parathyroid hormone secretion / mast cell differentiation / regulation of nephron tubule epithelial cell differentiation / regulation of epithelial cell differentiation / positive regulation of signal transduction / lymphocyte migration / mesonephros development / ear development / Formation of the nephric duct / positive regulation of T-helper 2 cell cytokine production / positive regulation of transcription regulatory region DNA binding / regulation of T-helper cell differentiation / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / pharyngeal system development / cellular response to BMP stimulus / sympathetic nervous system development / negative regulation of cell motility / cell fate determination / T-helper 2 cell differentiation / aortic valve morphogenesis / cartilage development / regulation of establishment of cell polarity / lens development in camera-type eye / embryonic hemopoiesis / inner ear morphogenesis / ventricular septum development / positive regulation of T cell differentiation / negative regulation of epithelial to mesenchymal transition / negative regulation of interleukin-2 production / positive regulation of interleukin-4 production / regulation of neuron projection development / E-box binding / uterus development / macrophage differentiation / negative regulation of type II interferon production / humoral immune response / negative regulation of cell cycle / T cell differentiation / developmental growth / cell fate commitment / anatomical structure morphogenesis / embryonic organ development / TOR signaling / canonical Wnt signaling pathway / cellular response to interleukin-4 / cis-regulatory region sequence-specific DNA binding / regulation of neuron apoptotic process / negative regulation of endothelial cell apoptotic process / cell maturation / regulation of cytokine production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of endothelial cell migration / post-embryonic development / thymus development / erythrocyte differentiation / kidney development / axon guidance / neuron migration / response to virus / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / positive regulation of miRNA transcription / defense response / response to estrogen / male gonad development / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / RUNX1 regulates transcription of genes involved in differentiation of HSCs / T cell receptor signaling pathway / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsChen, Y. / Bates, D.L. / Dey, R. / Chen, L.
CitationJournal: Cell Rep / Year: 2012
Title: DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation.
Authors: Chen, Y. / Bates, D.L. / Dey, R. / Chen, P.H. / Machado, A.C. / Laird-Offringa, I.A. / Rohs, R. / Chen, L.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Nov 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 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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
A: Trans-acting T-cell-specific transcription factor GATA-3
W: DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
X: DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')
B: Trans-acting T-cell-specific transcription factor GATA-3
Y: DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
Z: DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,57910
Polymers50,3186
Non-polymers2624
Water3,837213
1
A: Trans-acting T-cell-specific transcription factor GATA-3
W: DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
X: DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2905
Polymers25,1593
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-24 kcal/mol
Surface area14370 Å2
MethodPISA
2
B: Trans-acting T-cell-specific transcription factor GATA-3
Y: DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
Z: DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2905
Polymers25,1593
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-38 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.765, 65.373, 72.922
Angle α, β, γ (deg.)90.000, 96.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Trans-acting T-cell-specific transcription factor GATA-3 / GATA-binding factor 3


Mass: 12893.872 Da / Num. of mol.: 2 / Fragment: UNP residues 260 -365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATA3 / Production host: Escherichia coli (E. coli) / References: UniProt: P23771
#2: DNA chain DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')


Mass: 6085.982 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#3: DNA chain DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')


Mass: 6179.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 3.13 Å3/Da / Density % sol: 60.74 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 15755

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1608
RfactorNum. reflection% reflection
Rfree0.2635 1548 8.6 %
Rwork0.2264 --
obs-15755 87.4 %
Solvent computationBsol: 43.8628 Å2
Displacement parametersBiso max: 142.47 Å2 / Biso mean: 60.6446 Å2 / Biso min: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1-9.52 Å20 Å2-12.669 Å2
2--4.943 Å20 Å2
3----14.462 Å2
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1597 1628 4 213 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_scbond_it2.3182
X-RAY DIFFRACTIONc_mcangle_it3.2032
X-RAY DIFFRACTIONc_scangle_it3.9062.5
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
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

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