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- PDB-6qhd: Lysine acetylated and tyrosine phosphorylated STAT3 in a complex ... -

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Basic information

Entry
Database: PDB / ID: 6qhd
TitleLysine acetylated and tyrosine phosphorylated STAT3 in a complex with DNA
Components
  • DNA (5'-D(*AP*AP*GP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*TP*GP*C)-3')
  • 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 / Lysine Acetylation / DNA Binding / Post Translational Modification / non canonical Amino Acid
Function / homology
Function and homology information


RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / radial glial cell differentiation / retinal rod cell differentiation / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / negative regulation of neuron migration / T-helper 17 type immune response ...RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / radial glial cell differentiation / retinal rod cell differentiation / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / negative regulation of neuron migration / T-helper 17 type immune response / Signalling to STAT3 / negative regulation of inflammatory response to wounding / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / cell surface receptor signaling pathway via STAT / primary miRNA binding / response to leptin / sexual reproduction / interleukin-11-mediated signaling pathway / regulation of feeding behavior / intracellular receptor signaling pathway / cellular response to interleukin-17 / T-helper 17 cell lineage commitment / Interleukin-9 signaling / Interleukin-21 signaling / Transcriptional regulation of pluripotent stem cells / interleukin-9-mediated signaling pathway / interleukin-10-mediated signaling pathway / MET activates STAT3 / interleukin-2-mediated signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / interleukin-15-mediated signaling pathway / interleukin-23-mediated signaling pathway / cellular response to leptin stimulus / negative regulation of stem cell differentiation / STAT3 nuclear events downstream of ALK signaling / astrocyte differentiation / Interleukin-23 signaling / Signaling by cytosolic FGFR1 fusion mutants / positive regulation of cytokine production involved in inflammatory response / Interleukin-15 signaling / Interleukin-37 signaling / Signaling by Leptin / Interleukin-27 signaling / negative regulation of glycolytic process / Interleukin-35 Signalling / growth hormone receptor signaling pathway / positive regulation of vascular endothelial cell proliferation / lncRNA binding / Signaling by ALK / temperature homeostasis / eating behavior / Interleukin-20 family signaling / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / Association of TriC/CCT with target proteins during biosynthesis / Interleukin-10 signaling / cell surface receptor signaling pathway via JAK-STAT / somatic stem cell population maintenance / positive regulation of interleukin-10 production / regulation of multicellular organism growth / positive regulation of vascular endothelial growth factor production / growth hormone receptor signaling pathway via JAK-STAT / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / phosphorylation / Nuclear events stimulated by ALK signaling in cancer / Growth hormone receptor signaling / signaling adaptor activity / Signaling by CSF3 (G-CSF) / energy homeostasis / cellular response to hormone stimulus / Interleukin-7 signaling / phosphatidylinositol 3-kinase/protein kinase B signal transduction / Downstream signal transduction / transforming growth factor beta receptor signaling pathway / negative regulation of autophagy / positive regulation of erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / mRNA transcription by RNA polymerase II / Signaling by SCF-KIT / PKR-mediated signaling / Cytoprotection by HMOX1 / Inactivation of CSF3 (G-CSF) signaling / chromatin DNA binding / defense response / cytokine-mediated signaling pathway / positive regulation of miRNA transcription / response to peptide hormone / negative regulation of inflammatory response / positive regulation of interleukin-6 production / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / protein import into nucleus / positive regulation of angiogenesis / Signaling by CSF1 (M-CSF) in myeloid cells / nuclear receptor activity / positive regulation of tumor necrosis factor production
Similarity search - Function
STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding domain / STAT3, SH2 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 transcription factor, all-alpha domain / STAT transcription factor, DNA-binding domain / STAT3, SH2 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 / 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 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / p53-like transcription factor, DNA-binding / 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 speciesHomo sapiens (human)
Murine adenovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsArbely, E. / Belo, Y. / Shahar, A. / Zarivach, R.
Funding support Israel, 1items
OrganizationGrant numberCountry
Israel Science Foundation807/15 Israel
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2019
Title: Unexpected implications of STAT3 acetylation revealed by genetic encoding of acetyl-lysine.
Authors: Belo, Y. / Mielko, Z. / Nudelman, H. / Afek, A. / Ben-David, O. / Shahar, A. / Zarivach, R. / Gordan, R. / Arbely, E.
History
DepositionJan 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 24, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,5424
Polymers147,5424
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-61 kcal/mol
Surface area56240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.491, 175.491, 79.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 136 - 715 / Label seq-ID: 10 - 589

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Signal transducer and activator of transcription 3 / Acute-phase response factor


Mass: 68256.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT3, APRF / Production host: Escherichia coli (E. coli) / References: UniProt: P40763
#2: DNA chain DNA (5'-D(*AP*AP*GP*AP*TP*TP*TP*AP*CP*GP*GP*GP*AP*AP*AP*TP*GP*C)-3')


Mass: 5588.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Murine adenovirus 1
#3: 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 / Source: (synth.) Murine adenovirus 1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1m Bis-Tris pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 430759 / Num. obs: 56525 / % possible obs: 99.7 % / Redundancy: 7.62 % / Rrim(I) all: 0.093 / Net I/σ(I): 10.22
Reflection shellResolution: 2.85→3.02 Å / Mean I/σ(I) obs: 0.97 / Num. unique obs: 8941 / CC1/2: 0.653 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BG1

1bg1


Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.842 / SU B: 51.55 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R: 0.655 / ESU R Free: 0.417 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34323 2781 4.9 %RANDOM
Rwork0.29391 ---
obs0.29651 53803 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 106.677 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å2-0 Å20 Å2
2--4.46 Å20 Å2
3----8.91 Å2
Refinement stepCycle: 1 / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8628 732 0 89 9449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199618
X-RAY DIFFRACTIONr_bond_other_d0.0030.028754
X-RAY DIFFRACTIONr_angle_refined_deg2.2321.89413137
X-RAY DIFFRACTIONr_angle_other_deg1.282320400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6651050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.1624.861397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.668151672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9951548
X-RAY DIFFRACTIONr_chiral_restr0.1190.21446
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219873
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021867
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8622.4744236
X-RAY DIFFRACTIONr_mcbond_other1.8612.4734235
X-RAY DIFFRACTIONr_mcangle_it3.3763.6925271
X-RAY DIFFRACTIONr_mcangle_other3.3763.6935272
X-RAY DIFFRACTIONr_scbond_it1.0862.3315382
X-RAY DIFFRACTIONr_scbond_other1.0862.3315381
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0613.4567866
X-RAY DIFFRACTIONr_long_range_B_refined8.14942.21239870
X-RAY DIFFRACTIONr_long_range_B_other8.13942.15639851
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 34448 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.607 210 -
Rwork0.536 3992 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01-0.57351.09971.1258-0.40281.27410.10980.32660.0802-0.4069-0.0532-0.0775-0.02840.1808-0.05670.61720.01050.17970.5258-0.04531.4172-13.464-44.2447.178
22.0445-0.5854-1.15131.19420.42761.36540.12060.3506-0.1001-0.442-0.07770.08710.003-0.1973-0.04290.62580.0182-0.18180.52040.04931.4083-74.307-43.4797.199
31.35340.46150.21131.44420.35442.64810.0684-0.1155-0.0007-0.47910.0709-0.2591-0.0618-0.0152-0.13930.69240.1576-0.01550.34860.05441.5992-44.764-45.983.576
41.31940.3477-0.17872.978-0.91712.72950.0983-0.0693-0.0054-0.46790.03760.26210.0873-0.012-0.13590.63860.15690.02140.3305-0.05311.5037-43.014-41.8033.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A136 - 715
2X-RAY DIFFRACTION2B136 - 715
3X-RAY DIFFRACTION3C1001 - 1018
4X-RAY DIFFRACTION4D1001 - 1018

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