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- PDB-5nwx: Insight into the molecular recognition mechanism of the coactivat... -

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Basic information

Entry
Database: PDB / ID: 5nwx
TitleInsight into the molecular recognition mechanism of the coactivator NCoA1 by STAT6
Components
  • Nuclear receptor coactivator 1
  • Signal transducer and activator of transcription 6
KeywordsTRANSCRIPTION / NcoA1 / STAT6 / PAS-B domain / transactivation domain
Function / homology
Function and homology information


regulation of mast cell proliferation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of transcription cofactors / mammary gland morphogenesis / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / positive regulation of isotype switching to IgE isotypes / negative regulation of type 2 immune response / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...regulation of mast cell proliferation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / SUMOylation of transcription cofactors / mammary gland morphogenesis / Recycling of bile acids and salts / Synthesis of bile acids and bile salts / positive regulation of isotype switching to IgE isotypes / negative regulation of type 2 immune response / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / HATs acetylate histones / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / interleukin-4-mediated signaling pathway / Estrogen-dependent gene expression / isotype switching to IgE isotypes / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / mammary gland epithelial cell proliferation / male mating behavior / hypothalamus development / cellular response to Thyroglobulin triiodothyronine / progesterone receptor signaling pathway / growth hormone receptor signaling pathway via JAK-STAT / cell surface receptor signaling pathway via JAK-STAT / response to retinoic acid / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / histone acetyltransferase / estrogen receptor signaling pathway / lactation / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / Downstream signal transduction / response to progesterone / cerebellum development / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / mRNA transcription by RNA polymerase II / defense response / cerebral cortex development / response to peptide hormone / RNA polymerase II transcription regulator complex / transcription coactivator binding / male gonad development / cytokine-mediated signaling pathway / response to estradiol / regulation of cell population proliferation / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / protein phosphatase binding / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein dimerization activity / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
STAT6, C-terminal / STAT6, SH2 domain / STAT6 C-terminal / 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 ...STAT6, C-terminal / STAT6, SH2 domain / STAT6 C-terminal / 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 / Nuclear receptor coactivator 1 / PAS domain / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / p53-like transcription factor, DNA-binding / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Signal transducer and activator of transcription 6 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsRusso, L. / Giller, K. / Pfitzner, E. / Griesinger, C. / Becker, S.
Citation
Journal: Sci Rep / Year: 2017
Title: Insight into the molecular recognition mechanism of the coactivator NCoA1 by STAT6.
Authors: Russo, L. / Giller, K. / Pfitzner, E. / Griesinger, C. / Becker, S.
#1: Journal: Journal of Molecular Biology / Year: 2004
Title: Structure of the NCoA-1/SRC-1 PAS-B Domain Bound to the LXXLL Motif of the STAT6 Transactivation domain
Authors: Razeto, A. / Ramakrishnan, V. / Litterst, C.M. / Giller, K. / Griesinger, C. / Carlomagno, T. / Lakomek, N. / Heimburg, T. / Lodrini, M. / Pfitzner, E. / Becker, S.
#2: Journal: Acta Crystallographica Section D / Year: 2004
Title: Crystallization and preliminary crystallographic studies of the NCoA-1/SRC-1 PAS-B domain bound to the LXXLL motif of the STAT6 transactivation domain
Authors: Razeto, A. / Pfitzner, E. / Becker, S.
History
DepositionMay 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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
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: Nuclear receptor coactivator 1
B: Signal transducer and activator of transcription 6


Theoretical massNumber of molelcules
Total (without water)18,2652
Polymers18,2652
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-10 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.631, 61.631, 73.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Nuclear receptor coactivator 1 / NCoA-1 / Nuclear receptor coactivator protein 1 / mNRC-1 / Steroid receptor coactivator 1 / SRC-1


Mass: 14811.774 Da / Num. of mol.: 1 / Fragment: UNP residues 257-385 / Mutation: K343R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ncoa1, Src1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70365, histone acetyltransferase
#2: Protein/peptide Signal transducer and activator of transcription 6 / IL-4 Stat


Mass: 3452.837 Da / Num. of mol.: 1 / Fragment: UNP residues 783-814
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STAT6 / Production host: synthetic construct (others) / References: UniProt: P42226
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.25 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M sodium acetate, 0.1 M sodium cacodylate, pH 6.5, 30% PEG 8000, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.7 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 2.51→53.37 Å / Num. obs: 5471 / % possible obs: 99.8 % / Redundancy: 20.51 % / Rrim(I) all: 0.0246 / Net I/σ(I): 30.26
Reflection shellResolution: 2.51→2.61 Å / Redundancy: 19.92 % / Mean I/σ(I) all: 6.08 / Rrim(I) all: 0.1315 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OJ5

1oj5


Resolution: 2.51→53.37 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.917 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.341 / ESU R Free: 0.248 / Stereochemistry target values: Maximum likelihood / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23546 245 4.5 %RANDOM
Rwork0.18352 ---
obs0.18595 5203 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å20.59 Å20 Å2
2--1.19 Å20 Å2
3----1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.51→53.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms868 0 0 8 876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9671211
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4475114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80523.33333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20815142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.244155
X-RAY DIFFRACTIONr_chiral_restr0.1240.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021661
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 11 -
Rwork0.258 359 -
obs--96.86 %

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