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- PDB-4e68: Unphosphorylated STAT3B core protein binding to dsDNA -

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Basic information

Entry
Database: PDB / ID: 4.0E+68
TitleUnphosphorylated STAT3B core protein binding to dsDNA
Components
  • DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
  • Signal transducer and activator of transcription 3
KeywordsTRANSCRIPTION/DNA / SH2 Domain / Protein DNA Complex / Signal Transducer / Activator of Transcription / Duplex DNA / Nucleus / Cytosol / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


STAT3 nuclear events downstream of ALK signaling / MET activates STAT3 / Interleukin-37 signaling / Interleukin-10 signaling / PTK6 Activates STAT3 / Signaling by ALK / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling ...STAT3 nuclear events downstream of ALK signaling / MET activates STAT3 / Interleukin-37 signaling / Interleukin-10 signaling / PTK6 Activates STAT3 / Signaling by ALK / Interleukin-21 signaling / RNA sequestering activity / Interleukin-9 signaling / Interleukin-4 and Interleukin-13 signaling / Interleukin-15 signaling / Interleukin-20 family signaling / Interleukin-23 signaling / Interleukin-27 signaling / Interleukin-6 signaling / radial glial cell differentiation / retinal rod cell differentiation / Downstream signal transduction / Interleukin-35 Signalling / negative regulation of primary miRNA processing / Interleukin-7 signaling / Signaling by SCF-KIT / leptin-mediated signaling pathway / T-helper 17 type immune response / negative regulation of neuron migration / PKR-mediated signaling / response to leptin / negative regulation of inflammatory response to wounding / interleukin-10-mediated signaling pathway / primary miRNA binding / interleukin-11-mediated signaling pathway / cellular response to interleukin-17 / T-helper 17 cell lineage commitment / sexual reproduction / regulation of feeding behavior / interleukin-9-mediated signaling pathway / interleukin-2-mediated signaling pathway / interleukin-23-mediated signaling pathway / acetylation-dependent protein binding / cellular response to leptin stimulus / interleukin-15-mediated signaling pathway / astrocyte differentiation / negative regulation of stem cell differentiation / positive regulation of cytokine production involved in inflammatory response / negative regulation of glycolytic process / positive regulation of vascular endothelial cell proliferation / phosphorylation / temperature homeostasis / interleukin-6-mediated signaling pathway / eating behavior / lncRNA binding / positive regulation of Notch signaling pathway / cellular response to cytokine stimulus / : / positive regulation of interleukin-10 production / somatic stem cell population maintenance / growth hormone receptor signaling pathway via JAK-STAT / positive regulation of vascular endothelial growth factor production / regulation of multicellular organism growth / cell surface receptor signaling pathway via JAK-STAT / energy homeostasis / negative regulation of canonical NF-kappaB signal transduction / signaling adaptor activity / negative regulation of cytokine production involved in inflammatory response / transforming growth factor beta receptor signaling pathway / negative regulation of autophagy / protein sequestering activity / positive regulation of erythrocyte differentiation / positive regulation of interleukin-1 beta production / acute-phase response / positive regulation of interleukin-8 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA transcription by RNA polymerase II / cytokine-mediated signaling pathway / chromatin DNA binding / positive regulation of miRNA transcription / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / protein import into nucleus / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / glucose homeostasis / response to estradiol / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / gene expression / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / transcription cis-regulatory region binding / regulation of cell cycle / protein dimerization activity / positive regulation of cell migration / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
STAT3, SH2 domain / STAT transcription factor, DNA-binding domain / STAT transcription factor, all-alpha 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 transcription factor, coiled-coil domain / STAT protein, DNA binding domain ...STAT3, SH2 domain / STAT transcription factor, DNA-binding domain / STAT transcription factor, all-alpha 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 transcription factor, coiled-coil domain / STAT protein, DNA binding domain / STAT protein, protein interaction domain / Signal transducer and activator of transcription, linker domain / STAT protein, protein interaction domain / STAT transcription factor, N-terminal domain superfamily / Transcription factor STAT / STAT transcription factor, coiled coil / SH2 domain / SHC Adaptor Protein / p53-like transcription factor, DNA-binding / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / EF-hand / Recoverin; domain 1 / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.585 Å
AuthorsCollie, G.W. / Parkinson, G.N. / Shah, R.
CitationJournal: Febs Lett. / Year: 2013
Title: Observation of unphosphorylated STAT3 core protein binding to target dsDNA by PEMSA and X-ray crystallography.
Authors: Nkansah, E. / Shah, R. / Collie, G.W. / Parkinson, G.N. / Palmer, J. / Rahman, K.M. / Bui, T.T. / Drake, A.F. / Husby, J. / Neidle, S. / Zinzalla, G. / Thurston, D.E. / Wilderspin, A.F.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references
Revision 1.3Sep 13, 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 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,5772
Polymers73,5772
Non-polymers00
Water2,504139
1
B: DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
A: Signal transducer and activator of transcription 3

B: DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')
A: Signal transducer and activator of transcription 3


Theoretical massNumber of molelcules
Total (without water)147,1534
Polymers147,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-y+1,z1
Buried area6670 Å2
ΔGint-61 kcal/mol
Surface area59930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.140, 174.140, 79.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: DNA chain DNA (5'-D(*TP*GP*CP*AP*TP*TP*TP*CP*CP*CP*GP*TP*AP*AP*AP*TP*CP*T)-3')


Mass: 5441.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesised DNA sequence / Source: (synth.) Synthetic (others)
#2: Protein Signal transducer and activator of transcription 3 / Acute-phase response factor


Mass: 68135.125 Da / Num. of mol.: 1 / Fragment: STAT3 Core Fragment, residues (127-722)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aprf, Stat3, STAT3B / Plasmid: pET-32a (+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: P42227
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO ISOFORM STAT3B

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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: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.005M MgSO4, 0.1M ammonium acetate, 10% glycerol, 0.05M MES pH 5.6, 0.25M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 16, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.58→72.16 Å / Num. all: 36458 / Num. obs: 36458 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 75.03 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.2
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2721 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0117refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BG1

1bg1


Resolution: 2.585→14.98 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.223 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27332 1810 5 %RANDOM
Rwork0.22532 ---
obs0.22778 34413 97.08 %-
all-34413 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.881 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.585→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4499 360 0 139 4998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194987
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9116810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2035556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.65224.928209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97415869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6731525
X-RAY DIFFRACTIONr_chiral_restr0.1260.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213569
LS refinement shellResolution: 2.585→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 137 -
Rwork0.361 2420 -
obs-2420 99.22 %

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