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- PDB-4hca: DNA binding by GATA transcription factor-complex 1 -

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Basic information

Entry
Database: PDB / ID: 4hca
TitleDNA binding by GATA transcription factor-complex 1
Components
  • DNA (5'-D(*AP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*CP*G)-3')
  • DNA (5'-D(*TP*TP*CP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*A)-3')
  • Trans-acting T-cell-specific transcription factor GATA-3
KeywordsTranscription/DNA / zinc finger / GATA transcription factor / DNA bridging / 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 / : ...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 / anatomical structure formation involved in morphogenesis / pro-T cell differentiation / negative regulation of mammary gland epithelial cell proliferation / nephric duct morphogenesis / interleukin-2 receptor binding / norepinephrine biosynthetic process / cardiac right ventricle morphogenesis / cellular response to interferon-alpha / immune system development / parathyroid gland development / ureter maturation / mesenchymal to epithelial transition / mast cell differentiation / parathyroid hormone secretion / regulation of nephron tubule epithelial cell differentiation / regulation of epithelial cell differentiation / positive regulation of signal transduction / lymphocyte migration / mesonephros development / Formation of the nephric duct / positive regulation of T-helper 2 cell cytokine production / regulation of T-helper cell differentiation / ear development / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / pharyngeal system development / sympathetic nervous system development / negative regulation of cell motility / cellular response to BMP stimulus / cell fate determination / positive regulation of transcription regulatory region DNA binding / negative regulation of epithelial to mesenchymal transition / T-helper 2 cell differentiation / aortic valve morphogenesis / cartilage development / regulation of establishment of cell polarity / lens development in camera-type eye / positive regulation of T cell differentiation / embryonic hemopoiesis / ventricular septum development / negative regulation of interleukin-2 production / regulation of neuron projection development / inner ear morphogenesis / positive regulation of interleukin-4 production / E-box binding / uterus development / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / negative regulation of cell cycle / T cell differentiation / developmental growth / TOR signaling / anatomical structure morphogenesis / canonical Wnt signaling pathway / cell fate commitment / embryonic organ development / cellular response to interleukin-4 / cis-regulatory region sequence-specific DNA binding / negative regulation of endothelial cell apoptotic process / regulation of neuron apoptotic process / cell maturation / regulation of cytokine production / positive regulation of endothelial cell migration / erythrocyte differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / post-embryonic development / thymus development / kidney development / axon guidance / neuron migration / response to virus / defense response / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory 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 / Estrogen-dependent gene expression
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 / Resolution: 2.8 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 1.2Feb 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_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
X: DNA (5'-D(*AP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*CP*G)-3')
Y: DNA (5'-D(*TP*TP*CP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2915
Polymers25,1603
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-27 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.486, 36.550, 66.118
Angle α, β, γ (deg.)90.000, 103.700, 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.: 1 / Fragment: UNP residues 260 -368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23771
#2: DNA chain DNA (5'-D(*AP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*AP*TP*AP*AP*GP*AP*CP*G)-3')


Mass: 6142.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#3: DNA chain DNA (5'-D(*TP*TP*CP*GP*TP*CP*TP*TP*AP*TP*CP*AP*GP*AP*TP*GP*GP*AP*CP*A)-3')


Mass: 6123.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 6371 / Biso Wilson estimate: 58.61 Å2

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→28.766 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.6514 / SU ML: 0.4 / σ(F): 1.35 / Phase error: 38.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2956 294 4.61 %
Rwork0.2446 --
obs0.2471 6371 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.732 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 476.88 Å2 / Biso mean: 73.412 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--13.6666 Å20 Å2-8.8682 Å2
2--3.0993 Å20 Å2
3----5.6005 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 814 2 0 1591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061701
X-RAY DIFFRACTIONf_angle_d1.2682467
X-RAY DIFFRACTIONf_chiral_restr0.054272
X-RAY DIFFRACTIONf_plane_restr0.004178
X-RAY DIFFRACTIONf_dihedral_angle_d27.258689
LS refinement shellResolution: 2.8→3.5272 Å / Total num. of bins used: 2
RfactorNum. reflection% reflection
Rfree0.3641 142 -
Rwork0.3127 3008 -
all-3150 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -5.5418 Å / Origin y: -7.7538 Å / Origin z: -16.7086 Å
111213212223313233
T0.4726 Å20.1296 Å20.0013 Å2-0.433 Å2-0.0298 Å2--0.3311 Å2
L0.6127 °21.6657 °20.3963 °2-0.9499 °2-0.117 °2--3.5043 °2
S-0.058 Å °0.5304 Å °-0.2046 Å °-0.0038 Å °-0.2018 Å °0.0531 Å °-0.1497 Å °0.0373 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA260 - 369
2X-RAY DIFFRACTION1allX1 - 20
3X-RAY DIFFRACTION1allY1 - 20
4X-RAY DIFFRACTION1allA30 - 402

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