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- PDB-1y1u: Structure of unphosphorylated STAT5a -

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Basic information

Entry
Database: PDB / ID: 1y1u
TitleStructure of unphosphorylated STAT5a
ComponentsSignal transducer and activator of transcription 5A
KeywordsSIGNALING PROTEIN / Activator / STAT / DNA-binding / SH2 domain / Transcription regulation
Function / homology
Function and homology information


positive regulation of mast cell differentiation / development of secondary female sexual characteristics / Nuclear signaling by ERBB4 / Interleukin-2 signaling / Interleukin-21 signaling / Interleukin-9 signaling / Growth hormone receptor signaling / development of secondary male sexual characteristics / negative regulation of mast cell apoptotic process / Interleukin-15 signaling ...positive regulation of mast cell differentiation / development of secondary female sexual characteristics / Nuclear signaling by ERBB4 / Interleukin-2 signaling / Interleukin-21 signaling / Interleukin-9 signaling / Growth hormone receptor signaling / development of secondary male sexual characteristics / negative regulation of mast cell apoptotic process / Interleukin-15 signaling / Interleukin-20 family signaling / positive regulation of natural killer cell differentiation / negative regulation of erythrocyte differentiation / Downstream signal transduction / Interleukin-7 signaling / taurine metabolic process / Signaling by SCF-KIT / positive regulation of mast cell proliferation / regulation of epithelial cell differentiation / luteinization / reelin-mediated signaling pathway / mammary gland involution / natural killer cell differentiation / positive regulation of gamma-delta T cell differentiation / positive regulation of lymphocyte differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / regulation of steroid metabolic process / mammary gland epithelium development / lipid storage / Peyer's patch development / epithelial cell differentiation involved in prostate gland development / prostate gland epithelium morphogenesis / mammary gland development / positive regulation of multicellular organism growth / cellular response to granulocyte macrophage colony-stimulating factor stimulus / positive regulation of B cell differentiation / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of activated T cell proliferation / phosphate ion binding / T cell homeostasis / cellular response to cytokine stimulus / cell surface receptor signaling pathway via JAK-STAT / cellular response to organic cyclic compound / regulation of multicellular organism growth / positive regulation of blood vessel endothelial cell migration / growth hormone receptor signaling pathway via JAK-STAT / regulation of cell adhesion / positive regulation of interleukin-2 production / lactation / positive regulation of endothelial cell proliferation / positive regulation of mitotic cell cycle / female pregnancy / defense response / response to peptide hormone / positive regulation of inflammatory response / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / T cell differentiation in thymus / regulation of cell population proliferation / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
STAT5a/5b / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding 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 ...STAT5a/5b / STAT transcription factor, all-alpha domain / STAT transcription factor, DNA-binding 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 / 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. / Src homology 2 domains / 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
Signal transducer and activator of transcription 5A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsNeculai, D. / Neculai, A.M. / Verrier, S. / Straub, K. / Klumpp, K. / Pfitzner, E. / Becker, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structure of the unphosphorylated STAT5a dimer
Authors: Neculai, D. / Neculai, A.M. / Verrier, S. / Straub, K. / Klumpp, K. / Pfitzner, E. / Becker, S.
History
DepositionNov 19, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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_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.end_auth_comp_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)201,7783
Polymers201,7783
Non-polymers00
Water0
1
A: Signal transducer and activator of transcription 5A
B: Signal transducer and activator of transcription 5A


Theoretical massNumber of molelcules
Total (without water)134,5192
Polymers134,5192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Signal transducer and activator of transcription 5A

C: Signal transducer and activator of transcription 5A


Theoretical massNumber of molelcules
Total (without water)134,5192
Polymers134,5192
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Unit cell
Length a, b, c (Å)143.020, 235.430, 111.420
Angle α, β, γ (deg.)90.00, 108.76, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 138 - 688 / Label seq-ID: 11 - 561

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein Signal transducer and activator of transcription 5A / STAT5a / Mammary gland factor


Mass: 67259.414 Da / Num. of mol.: 3 / Fragment: STAT5a core fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42230

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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: 4.4 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M (NH4)2SO4, 20mM MgCl2, 10% glycerol, 50mM HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 18, 2004 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.21→90 Å / Num. all: 56837 / Num. obs: 56787 / % possible obs: 99.9 % / Observed criterion σ(F): 3.03 / Observed criterion σ(I): 2.49 / Redundancy: 1.98 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.0882 / Rsym value: 0.104 / Net I/σ(I): 9.82
Reflection shellResolution: 3.21→3.25 Å / Redundancy: 1.99 % / Rmerge(I) obs: 0.3148 / Mean I/σ(I) obs: 2.49 / Num. unique all: 2076 / Rsym value: 0.4161 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
PHASERV. 1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BG1

1bg1


Resolution: 3.21→78.56 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.802 / SU B: 51.006 / SU ML: 0.399 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 5.53 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29891 5010 8.9 %RANDOM
Rwork0.26619 ---
obs0.26909 51051 98.64 %-
all-56837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.774 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.09 Å2
2--0 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 3.21→78.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13293 0 0 0 13293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02213581
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.94318402
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.93951626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37725.086696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.852152457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7691578
X-RAY DIFFRACTIONr_chiral_restr0.1280.22034
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210308
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2680.27508
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.29236
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.340.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0390.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5741.58329
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.041213233
X-RAY DIFFRACTIONr_scbond_it1.0635897
X-RAY DIFFRACTIONr_scangle_it1.8324.55169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4426 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.030.05
1Atight thermal0.050.5
2Btight thermal0.050.5
3Ctight thermal0.050.5
LS refinement shellResolution: 3.21→3.293 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 335 -
Rwork0.343 3776 -
obs--97.95 %
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)
12.18921.3754-0.20351.393-0.16360.3208-0.0511-0.02610.01210.0970.0006-0.0244-0.1220.07230.0505-0.0888-0.02550.0705-0.0898-0.0049-0.1884-59.326724.372827.5978
20.65631.079-0.25653.1784-0.71960.2026-0.03420.0556-0.05450.013-0.01050.03720.03960.01580.0447-0.0505-0.04970.0289-0.11960.0299-0.1798-31.086649.9716-9.7919
31.6073-0.49031.23730.627-0.41021.20420.0777-0.01380.00630.1075-0.08290.0233-0.03160.00430.0053-0.1151-0.01340.0124-0.00240.0405-0.2114-64.552385.235525.7767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA138 - 67411 - 547
2X-RAY DIFFRACTION2BB138 - 67411 - 547
3X-RAY DIFFRACTION3CC138 - 67411 - 547

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