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- PDB-5d39: Transcription factor-DNA complex -

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Basic information

Entry
Database: PDB / ID: 5d39
TitleTranscription factor-DNA complex
Components
  • DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*GP*GP*AP*AP*GP*AP*CP*AP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*TP*GP*TP*CP*TP*TP*CP*CP*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 / 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
DNA / DNA (> 10) / Signal transducer and activator of transcription 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 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 1.4Aug 30, 2017Group: Data collection / Database references / Category: citation / diffrn_detector / Item: _citation.journal_id_CSD / _diffrn_detector.detector
Revision 1.5Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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

Downloads & links

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Assembly

Deposited unit
A: Signal transducer and activator of transcription 6
B: Signal transducer and activator of transcription 6
C: Signal transducer and activator of transcription 6
D: Signal transducer and activator of transcription 6
N: DNA (5'-D(P*TP*CP*TP*GP*TP*CP*TP*TP*CP*CP*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*GP*GP*AP*AP*GP*AP*CP*AP*GP*A)-3')
E: DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*GP*GP*AP*AP*GP*AP*CP*AP*GP*A)-3')
F: DNA (5'-D(P*TP*CP*TP*GP*TP*CP*TP*TP*CP*CP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)266,9018
Polymers266,9018
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13800 Å2
ΔGint-105 kcal/mol
Surface area109370 Å2
2
A: Signal transducer and activator of transcription 6
C: Signal transducer and activator of transcription 6
N: DNA (5'-D(P*TP*CP*TP*GP*TP*CP*TP*TP*CP*CP*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*GP*GP*AP*AP*GP*AP*CP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)133,4504
Polymers133,4504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-53 kcal/mol
Surface area54770 Å2
MethodPISA
3
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*GP*GP*AP*AP*GP*AP*CP*AP*GP*A)-3')
F: DNA (5'-D(P*TP*CP*TP*GP*TP*CP*TP*TP*CP*CP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)133,4504
Polymers133,4504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-52 kcal/mol
Surface area55700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.395, 94.697, 145.642
Angle α, β, γ (deg.)79.62, 78.31, 89.58
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: 60283.043 Da / Num. of mol.: 4 / Fragment: UNP residues 123-658
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT6 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42226
#2: DNA chain DNA (5'-D(P*TP*CP*TP*GP*TP*CP*TP*TP*CP*CP*AP*GP*GP*AP*AP*AP*TP*CP*CP*AP*T)-3')


Mass: 6373.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*AP*TP*GP*GP*AP*TP*TP*TP*CP*CP*TP*GP*GP*AP*AP*GP*AP*CP*AP*GP*A)-3')


Mass: 6511.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citrate (pH 5.6), 0.1 M NaCl, 20% isopropyl alcohol and 8% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→44.12 Å / Num. obs: 57110 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 16.7
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.695 / Rsym value: 0.695 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
HKL-2000data processing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y5U

4y5u


Resolution: 3.2→44.12 Å / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.77 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2361 3118 2.76 %
Rwork0.2103 --
obs0.2111 57110 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15469 1722 0 206 17397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617677
X-RAY DIFFRACTIONf_angle_d1.32124207
X-RAY DIFFRACTIONf_dihedral_angle_d21.3526821
X-RAY DIFFRACTIONf_chiral_restr0.0542726
X-RAY DIFFRACTIONf_plane_restr0.0072814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2004-3.25560.37021460.33475592X-RAY DIFFRACTION94
3.2556-3.31480.3251450.30945358X-RAY DIFFRACTION94
3.3148-3.37850.29551490.3045493X-RAY DIFFRACTION94
3.3785-3.44750.3031600.28465499X-RAY DIFFRACTION94
3.4475-3.52240.27981280.27585427X-RAY DIFFRACTION94
3.5224-3.60430.31381480.26415498X-RAY DIFFRACTION94
3.6043-3.69440.28111550.26375402X-RAY DIFFRACTION94
3.6944-3.79420.25851580.245631X-RAY DIFFRACTION95
3.7942-3.90580.2931380.23925415X-RAY DIFFRACTION95
3.9058-4.03180.27761580.23065520X-RAY DIFFRACTION94
4.0318-4.17580.25281400.20725474X-RAY DIFFRACTION95
4.1758-4.34280.20281630.20455526X-RAY DIFFRACTION95
4.3428-4.54030.23071470.1935570X-RAY DIFFRACTION96
4.5403-4.77940.17731490.18085461X-RAY DIFFRACTION96
4.7794-5.07840.2381530.19165582X-RAY DIFFRACTION95
5.0784-5.46990.22741530.21535474X-RAY DIFFRACTION95
5.4699-6.01910.2341400.21035518X-RAY DIFFRACTION95
6.0191-6.88730.25771510.22395554X-RAY DIFFRACTION95
6.8873-8.66640.17921490.17825457X-RAY DIFFRACTION94
8.6664-44.12470.20671410.15765347X-RAY DIFFRACTION92

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