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- PDB-4y5w: Transcription factor-DNA complex -

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Basic information

Entry
Database: PDB / ID: 4y5w
TitleTranscription factor-DNA complex
Components
  • DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
  • Signal transducer and activator of transcription 6
KeywordsTRANSCRIPTION/DNA / regulation / DNA binding / innate immune / TRANSCRIPTION-DNA complex
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 / response to peptide hormone / defense response / cytokine-mediated signaling pathway / transcription coactivator binding / cellular response to hydrogen peroxide / 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
DNA / DNA (> 10) / Signal transducer and activator of transcription 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 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 1.1Mar 2, 2016Group: Data collection
Revision 1.2Nov 2, 2016Group: Database references
Revision 1.3Nov 16, 2016Group: Database references
Revision 1.4Nov 30, 2016Group: Database references
Revision 1.5Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 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
D: Signal transducer and activator of transcription 6
E: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
M: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
N: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
C: Signal transducer and activator of transcription 6


Theoretical massNumber of molelcules
Total (without water)273,3148
Polymers273,3148
Non-polymers00
Water4,161231
1
A: Signal transducer and activator of transcription 6
M: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
N: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')
C: Signal transducer and activator of transcription 6


Theoretical massNumber of molelcules
Total (without water)136,6574
Polymers136,6574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Signal transducer and activator of transcription 6
D: Signal transducer and activator of transcription 6
E: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)136,6574
Polymers136,6574
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.298, 94.241, 147.785
Angle α, β, γ (deg.)99.85, 101.73, 89.93
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 61577.602 Da / Num. of mol.: 4 / 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) / References: UniProt: P42226
#2: DNA chain DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*GP*AP*CP*AP*A)-3')


Mass: 6824.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*GP*TP*CP*TP*TP*CP*CP*TP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')


Mass: 6677.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.17 Å3/Da / Density % sol: 62.65 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M citrate (pH 5.6), 0.1M NaCl, 20% isopropyl alcohol and 8% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 57478 / % possible obs: 98 % / Redundancy: 3.5 % / Rsym value: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.65 / Rsym value: 0.4 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
PHENIXmodel building
PHASERphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5U

4y5u


Resolution: 3.104→38.807 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.278 2918 5.08 %
Rwork0.2496 --
obs0.2511 57478 89.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.104→38.807 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15038 1804 0 231 17073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817347
X-RAY DIFFRACTIONf_angle_d1.06423773
X-RAY DIFFRACTIONf_dihedral_angle_d19.3836666
X-RAY DIFFRACTIONf_chiral_restr0.0452683
X-RAY DIFFRACTIONf_plane_restr0.0062733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1038-3.15460.3618840.34511473X-RAY DIFFRACTION51
3.1546-3.2090.3594940.32531750X-RAY DIFFRACTION61
3.209-3.26730.3393810.31811997X-RAY DIFFRACTION67
3.2673-3.33010.37011040.31582095X-RAY DIFFRACTION72
3.3301-3.39810.32441210.30542239X-RAY DIFFRACTION77
3.3981-3.47190.36021330.29172442X-RAY DIFFRACTION85
3.4719-3.55260.30531310.27732646X-RAY DIFFRACTION91
3.5526-3.64140.29061510.27032860X-RAY DIFFRACTION97
3.6414-3.73980.32581740.26692783X-RAY DIFFRACTION98
3.7398-3.84970.27391570.26162821X-RAY DIFFRACTION98
3.8497-3.97390.25931480.24962903X-RAY DIFFRACTION98
3.9739-4.11580.2841400.24422838X-RAY DIFFRACTION98
4.1158-4.28030.30061700.23182879X-RAY DIFFRACTION98
4.2803-4.47490.22281450.23782858X-RAY DIFFRACTION98
4.4749-4.71040.22481410.21542840X-RAY DIFFRACTION98
4.7104-5.0050.26041460.22892873X-RAY DIFFRACTION99
5.005-5.39050.27811360.24532866X-RAY DIFFRACTION99
5.3905-5.93120.27421630.25712874X-RAY DIFFRACTION99
5.9312-6.78550.28931810.26882847X-RAY DIFFRACTION99
6.7855-8.5340.26921800.24232839X-RAY DIFFRACTION99
8.534-38.80960.23171380.20242837X-RAY DIFFRACTION98

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