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- PDB-4y5u: Transcription factor -

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Basic information

Entry
Database: PDB / ID: 4y5u
TitleTranscription factor
ComponentsSignal transducer and activator of transcription 6
KeywordsTRANSCRIPTION / dimerization / innate immune / DNA binding
Function / homology
Function and homology information


regulation of mast cell proliferation / mammary gland morphogenesis / cellular response to reactive nitrogen species / negative regulation of type 2 immune response / positive regulation of isotype switching to IgE isotypes / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / isotype switching to IgE isotypes / interleukin-4-mediated signaling pathway / mammary gland epithelial cell proliferation ...regulation of mast cell proliferation / mammary gland morphogenesis / cellular response to reactive nitrogen species / negative regulation of type 2 immune response / positive regulation of isotype switching to IgE isotypes / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / isotype switching to IgE isotypes / interleukin-4-mediated signaling pathway / mammary gland epithelial cell proliferation / cell surface receptor signaling pathway via JAK-STAT / growth hormone receptor signaling pathway via JAK-STAT / Downstream signal transduction / RNA polymerase II transcription regulatory region sequence-specific DNA binding / defense response / transcription coactivator binding / cellular response to hydrogen peroxide / response to peptide hormone / cytokine-mediated signaling pathway / RNA polymerase II transcription regulator complex / positive regulation of cold-induced thermogenesis / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
STAT6, C-terminal / STAT6, SH2 domain / STAT6 C-terminal / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain ...STAT6, C-terminal / STAT6, SH2 domain / STAT6 C-terminal / : / Signal transducer and activator of transcription, linker domain / STAT transcription factor, DNA-binding, N-terminal / STAT transcription factor, protein interaction / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding / STAT protein, all-alpha domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / p53-like transcription factor, DNA-binding / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Signal transducer and activator of transcription 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.708 Å
AuthorsLi, J. / Niu, F. / Ouyang, S. / Liu, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural basis for DNA recognition by STAT6
Authors: Li, J. / Rodriguez, J.P. / Niu, F. / Pu, M. / Wang, J. / Hung, L.W. / Shao, Q. / Zhu, Y. / Ding, W. / Liu, Y. / Da, Y. / Yao, Z. / Yang, J. / Zhao, Y. / Wei, G.H. / Cheng, G. / Liu, Z.J. / Ouyang, S.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Nov 30, 2016Group: Database references
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal transducer and activator of transcription 6
B: Signal transducer and activator of transcription 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,2143
Polymers123,1552
Non-polymers591
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-18 kcal/mol
Surface area43600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.152, 94.322, 179.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Signal transducer and activator of transcription 6 / IL-4 Stat


Mass: 61577.602 Da / Num. of mol.: 2 / Fragment: UNP residues 113-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT6 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42226
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M imidazole (pH 7.5), 0.2M Li2SO4, 12% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 28460 / % possible obs: 94.9 % / Redundancy: 5.2 % / Rsym value: 0.087 / Net I/σ(I): 17.68
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.516 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
PHENIXmodel building
PHASERphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y1U

1y1u


Resolution: 2.708→46.361 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 2000 7.03 %
Rwork0.1851 --
obs0.1899 28460 90.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.708→46.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7050 0 1 176 7227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087175
X-RAY DIFFRACTIONf_angle_d1.2379681
X-RAY DIFFRACTIONf_dihedral_angle_d19.6272702
X-RAY DIFFRACTIONf_chiral_restr0.0811099
X-RAY DIFFRACTIONf_plane_restr0.0051238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.708-2.77570.29451070.19721410X-RAY DIFFRACTION69
2.7757-2.85070.29691220.1971620X-RAY DIFFRACTION79
2.8507-2.93460.30171300.19711719X-RAY DIFFRACTION85
2.9346-3.02930.27691420.19781882X-RAY DIFFRACTION91
3.0293-3.13760.28691450.19161919X-RAY DIFFRACTION93
3.1376-3.26310.28341460.19481927X-RAY DIFFRACTION94
3.2631-3.41160.27741450.1961921X-RAY DIFFRACTION94
3.4116-3.59140.27361470.16641954X-RAY DIFFRACTION94
3.5914-3.81630.22541460.17071925X-RAY DIFFRACTION93
3.8163-4.11080.20831460.1581933X-RAY DIFFRACTION92
4.1108-4.52420.24121460.15631928X-RAY DIFFRACTION93
4.5242-5.17810.20371480.16761960X-RAY DIFFRACTION93
5.1781-6.5210.26911610.212123X-RAY DIFFRACTION99
6.521-46.3680.23561690.21852239X-RAY DIFFRACTION100

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