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- PDB-1oj5: Crystal structure of the Nco-A1 PAS-B domain bound to the STAT6 t... -

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Basic information

Entry
Database: PDB / ID: 1oj5
TitleCrystal structure of the Nco-A1 PAS-B domain bound to the STAT6 transactivation domain LXXLL motif
Components
  • SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6
  • STEROID RECEPTOR COACTIVATOR 1A
KeywordsTRANSCRIPTIONAL COACTIVATOR / COMPLEX / LXXLL MOTIF / TRANSCRIPTIONAL REGULATION / STAT6 / PAS DOMAIN / IL-4 STAT
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 / response to peptide hormone / cerebral cortex development / transcription coactivator binding / RNA polymerase II transcription regulator complex / 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 / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / 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 / cytoplasm / cytosol
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
IODIDE ION / : / 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 / OTHER / Resolution: 2.21 Å
AuthorsRazeto, A. / Ramakrishnan, V. / Giller, K. / Lakomek, N. / Carlomagno, T. / Griesinger, C. / Lodrini, M. / Litterst, C.M. / Pftizner, E. / Becker, S.
Citation
Journal: J.Mol.Biol. / 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.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: An Lxxll Motif in the Transactivation Domain of Stat6 Mediates Recruitment of Ncoa-1/Src-1
Authors: Litterst, C.M. / Pfitzner, E.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Transcriptional Activation by Stat6 Requires the Direct Interaction with Ncoa-1
Authors: Litterst, C.M. / Pfitzner, E.
History
DepositionJul 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STEROID RECEPTOR COACTIVATOR 1A
B: SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0577
Polymers16,4232
Non-polymers6355
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.100, 62.100, 73.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
DetailsTHIS BIOMOLECULE IS A HETERODIMERIC COMPLEX OF A PROTEINCHAIN WITH A PEPTIDE

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Components

#1: Protein STEROID RECEPTOR COACTIVATOR 1A / STEROID RECEPTOR COACTIVATOR-1 / NCOA1 / SRC1A


Mass: 14811.774 Da / Num. of mol.: 1 / Fragment: NCO-A1 PAS-B DOMAIN, RESIDUES 257-385 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Description: CELLULAR LOCATION\: NUCLEUS / Plasmid: PET16BTEV-NCOA-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O61202, UniProt: P70365*PLUS
#2: Protein/peptide SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 6 / IL-4 STAT


Mass: 1610.865 Da / Num. of mol.: 1 / Fragment: STAT6 LXXLL MOTIF, RESIDUES 795-808 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P42226
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE LYS(343)ARG
Sequence detailsRESIDUES A254-A256 ARE FROM THE VECTOR PET16BTEV

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7 / Details: 20 % PEG3350, 0.2 M LICL, pH 7.00
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES1droppH7.0
2150 mM1dropNaCl
32 mMdithiothreitol1drop
419 mg/mlprotein1drop
50.2 M1reservoirLiCl
620 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS M18X / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 24, 2003 / Details: OSMIC MIRRORS CMF12-38CU6
RadiationMonochromator: OSMIC MIRRORS CMF12-38CU6 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→19.21 Å / Num. obs: 8138 / % possible obs: 99.7 % / Redundancy: 16.8 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 29.9
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 16 % / Rmerge(I) obs: 0.3254 / Mean I/σ(I) obs: 8.71 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.21 Å / Lowest resolution: 19.2 Å / Redundancy: 16.8 % / Num. measured all: 137915 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 16 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 8.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: OTHER / Resolution: 2.21→19.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.825 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LAST RUN OF REFINEMENT WAS PERFORMED WITH ALL THE REFLECTIONS. THE R FREE REPORTED ABOVE IS REFERRED TO THE PREVIOUS RUN OF REFINEMENT. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LAST RUN OF REFINEMENT WAS PERFORMED WITH ALL THE REFLECTIONS. THE R FREE REPORTED ABOVE IS REFERRED TO THE PREVIOUS RUN OF REFINEMENT. SIDE CHAINS WITH POOR ELECTRON DENSITY WERE ASSIGNED OCCUPANCY 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.214 375 0.05 %RANDOM
Rwork0.166 ---
obs0.17 8138 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 32.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20.43 Å20 Å2
2--0.87 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.21→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 5 116 1039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021948
X-RAY DIFFRACTIONr_bond_other_d0.0020.02865
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9571281
X-RAY DIFFRACTIONr_angle_other_deg0.8132012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.795116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021027
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02192
X-RAY DIFFRACTIONr_nbd_refined0.1950.2184
X-RAY DIFFRACTIONr_nbd_other0.2370.2968
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.2567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8521.5594
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5922965
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.933354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1214.5316
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: 2.21→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.23 30
Rwork0.167 570
Refinement
*PLUS
Lowest resolution: 19.2 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.394

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