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- PDB-6mbw: Structure of Transcription Factor -

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Basic information

Entry
Database: PDB / ID: 6mbw
TitleStructure of Transcription Factor
ComponentsSignal transducer and activator of transcription 5B
KeywordsTRANSCRIPTION ACTIVATOR / transcription factor
Function / homology
Function and homology information


development of secondary female sexual characteristics / development of secondary male sexual characteristics / natural killer cell proliferation / positive regulation of natural killer cell differentiation / mast cell migration / negative regulation of erythrocyte differentiation / taurine metabolic process / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 ...development of secondary female sexual characteristics / development of secondary male sexual characteristics / natural killer cell proliferation / positive regulation of natural killer cell differentiation / mast cell migration / negative regulation of erythrocyte differentiation / taurine metabolic process / response to interleukin-2 / response to interleukin-15 / response to interleukin-4 / myeloid cell apoptotic process / regulation of epithelial cell differentiation / luteinization / gamma-delta T cell differentiation / natural killer cell differentiation / positive regulation of gamma-delta T cell differentiation / Interleukin-9 signaling / Interleukin-21 signaling / progesterone metabolic process / regulation of steroid metabolic process / lipid storage / STAT5 Activation / negative regulation of myeloid cell apoptotic process / nuclear glucocorticoid receptor binding / positive regulation of natural killer cell mediated cytotoxicity / Peyer's patch development / Erythropoietin activates STAT5 / natural killer cell mediated cytotoxicity / positive regulation of multicellular organism growth / activated T cell proliferation / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / Signaling by Leptin / Interleukin-2 signaling / positive regulation of natural killer cell proliferation / positive regulation of B cell differentiation / Interleukin-20 family signaling / STAT5 activation downstream of FLT3 ITD mutants / positive regulation of activated T cell proliferation / Prolactin receptor signaling / T cell homeostasis / cell surface receptor signaling pathway via JAK-STAT / regulation of multicellular organism growth / Interleukin-3, Interleukin-5 and GM-CSF signaling / growth hormone receptor signaling pathway via JAK-STAT / Growth hormone receptor signaling / Signaling by CSF3 (G-CSF) / cellular response to hormone stimulus / cellular response to epidermal growth factor stimulus / Signaling by FLT3 fusion proteins / positive regulation of interleukin-2 production / lactation / Interleukin-7 signaling / positive regulation of mitotic cell cycle / Downstream signal transduction / B cell differentiation / erythrocyte differentiation / positive regulation of erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / female pregnancy / Inactivation of CSF3 (G-CSF) signaling / Signaling by SCF-KIT / cellular response to growth factor stimulus / response to peptide hormone / defense response / cytokine-mediated signaling pathway / positive regulation of inflammatory response / RNA polymerase II transcription regulator complex / response to estradiol / mitotic cell cycle / T cell differentiation in thymus / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription by RNA polymerase II / protein dimerization activity / 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 binding / chromatin / regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
STAT5b, SH2 domain / STAT5a/5b / 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 ...STAT5b, SH2 domain / STAT5a/5b / 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
Signal transducer and activator of transcription 5B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.29 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2019
Title: Structural and functional consequences of the STAT5BN642H driver mutation.
Authors: de Araujo, E.D. / Erdogan, F. / Neubauer, H.A. / Meneksedag-Erol, D. / Manaswiyoungkul, P. / Eram, M.S. / Seo, H.S. / Qadree, A.K. / Israelian, J. / Orlova, A. / Suske, T. / Pham, H.T.T. / ...Authors: de Araujo, E.D. / Erdogan, F. / Neubauer, H.A. / Meneksedag-Erol, D. / Manaswiyoungkul, P. / Eram, M.S. / Seo, H.S. / Qadree, A.K. / Israelian, J. / Orlova, A. / Suske, T. / Pham, H.T.T. / Boersma, A. / Tangermann, S. / Kenner, L. / Rulicke, T. / Dong, A. / Ravichandran, M. / Brown, P.J. / Audette, G.F. / Rauscher, S. / Dhe-Paganon, S. / Moriggl, R. / Gunning, P.T.
History
DepositionAug 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal transducer and activator of transcription 5B
B: Signal transducer and activator of transcription 5B


Theoretical massNumber of molelcules
Total (without water)131,2392
Polymers131,2392
Non-polymers00
Water543
1
A: Signal transducer and activator of transcription 5B


Theoretical massNumber of molelcules
Total (without water)65,6191
Polymers65,6191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal transducer and activator of transcription 5B


Theoretical massNumber of molelcules
Total (without water)65,6191
Polymers65,6191
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.600, 138.620, 76.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Signal transducer and activator of transcription 5B


Mass: 65619.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT5B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51692
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 2.72 Å3/Da / Density % sol: 54.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.29→96.57 Å / Num. obs: 21977 / % possible obs: 98.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 114.29 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.87
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
3.29-3.386.91.0382137198.4
14.71-96.575.70.037197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y1U

1y1u


Resolution: 3.29→96.566 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3054 1150 5.23 %
Rwork0.2664 --
obs0.2684 21968 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→96.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7677 0 0 3 7680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027841
X-RAY DIFFRACTIONf_angle_d0.62610720
X-RAY DIFFRACTIONf_dihedral_angle_d3.14615
X-RAY DIFFRACTIONf_chiral_restr0.0411259
X-RAY DIFFRACTIONf_plane_restr0.0041386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.43980.41741590.34242541X-RAY DIFFRACTION99
3.4398-3.62110.38981750.32062545X-RAY DIFFRACTION99
3.6211-3.8480.40851250.31692562X-RAY DIFFRACTION97
3.848-4.14510.34111290.27362585X-RAY DIFFRACTION99
4.1451-4.56220.34211360.26632613X-RAY DIFFRACTION99
4.5622-5.22240.29991390.24722597X-RAY DIFFRACTION97
5.2224-6.57940.34381320.30582659X-RAY DIFFRACTION99
6.5794-96.60810.22091550.22832716X-RAY DIFFRACTION96

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