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

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Basic information

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


regulation of mast cell proliferation / mammary gland morphogenesis / cellular response to reactive nitrogen species / positive regulation of isotype switching to IgE isotypes / negative regulation of type 2 immune response / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / interleukin-4-mediated signaling pathway / isotype switching to IgE isotypes / labyrinthine layer morphogenesis ...regulation of mast cell proliferation / mammary gland morphogenesis / cellular response to reactive nitrogen species / positive regulation of isotype switching to IgE isotypes / negative regulation of type 2 immune response / T-helper 1 cell lineage commitment / STAT6-mediated induction of chemokines / interleukin-4-mediated signaling pathway / 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 / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / hypothalamus development / male mating behavior / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / growth hormone receptor signaling pathway via JAK-STAT / cell surface receptor signaling pathway via JAK-STAT / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / response to retinoic acid / progesterone receptor signaling pathway / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / cellular response to hormone stimulus / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / Recycling of bile acids and salts / histone acetyltransferase / estrous cycle / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / : / lactation / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / Downstream signal transduction / positive regulation of neuron differentiation / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / hippocampus development / response to progesterone / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / nuclear estrogen receptor binding / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / transcription coactivator binding / defense response / PPARA activates gene expression / cytokine-mediated signaling pathway / Cytoprotection by HMOX1 / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / response to peptide hormone / cellular response to hydrogen peroxide / RNA polymerase II transcription regulator complex / male gonad development / : / response to estradiol / regulation of cell population proliferation / HATs acetylate histones / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / protein phosphatase binding / Interleukin-4 and Interleukin-13 signaling / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / 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
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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsRusso, L. / Becker, S. / Griesinger, C.
CitationJournal: 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.
History
DepositionMay 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 19, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2090 Å2
ΔGint-20 kcal/mol
Surface area11670 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / 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.) Homo sapiens (human) / Gene: NCOA1, BHLHE74, SRC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15788, 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: Escherichia coli (E. coli) / References: UniProt: P42226

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic13D CBCA(CO)NH
141isotropic13D HNCA
151isotropic13D 1H-15N TOCSY
161isotropic23D 1H-15N NOESY
172isotropic12D 1H-15N HSQC
182isotropic32D 1H-13C HSQC aliphatic
192isotropic32D 1H-13C HSQC aromatic
1102isotropic33D CBCA(CO)NH
1112isotropic33D HNCO
1122isotropic43D HNCA
1132isotropic53D 1H-15N NOESY
1142isotropic33D 1H-15N TOCSY
1237isotropic53D 1H-13C NOESY aliphatic
1227isotropic53D 1H-13C NOESY aromatic
1212isotropic43D HNHA
1201isotropic23D HNHA
1197isotropic33D (H)CCH-TOCSY
1182isotropic43D HN(CA)CB
1173isotropic12D 1H-15N HSQC
1283isotropic32D 1H-13C HSQC aliphatic
1273isotropic32D 1H-13C HSQC aromatic
1263isotropic33D CBCA(CO)NH
1253isotropic33D HNCO
1243isotropic33D HNCA
1163isotropic53D 1H-15N NOESY
1153isotropic33D 1H-15N TOCSY
1328isotropic53D 1H-13C NOESY aliphatic
1318isotropic53D 1H-13C NOESY aromatic
1303isotropic33D HNHA
1298isotropic33D (H)CCH-TOCSY
1356anisotropic62D 1H-15N HSQC
1344anisotropic62D 1H-15N HSQC
1335anisotropic62D 1H-15N HSQC
1367isotropic43D 1H,13C-edited/12C-filter NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM HEPES, 150 mM sodium chloride, 10 % D2O, 1 mM [U-99% 13C; U-99% 15N] STAT6, 90% H2O/10% D2O15N,13C-STAT6783-81490% H2O/10% D2O
solution21 mM [U-99% 13C; U-99% 15N] STAT6, 0.7 mM NCoA1, 50 mM HEPES, 150 mM sodium chloride, 10 % D2O, 90% H2O/10% D2O15N,13C- STAT6783-814/NCoA1257-38590% H2O/10% D2O
solution30.7 mM [U-99% 13C; U-99% 15N] NCoA1, 1 mM STAT6, 50 mM HEPES, 150 mM sodium chloride, 10 % D2O, 90% H2O/10% D2O15N,13C NCoA1257-385/STAT6783-81490% H2O/10% D2O
filamentous virus41 mM [U-99% 15N] STAT6, 0.7 mM NCoA1, 50 mM HEPES, 150 mM sodium chloride, 10 % D2O, 90% H2O/10% D2ORDC15N-STAT6783-814/NCoA190% H2O/10% D2O
filamentous virus50.7 mM [U-99% 15N] NCoA1, 1 mM STAT6, 50 mM HEPES, 150 mM sodium chloride, 10 % D2O, 90% H2O/10% D2ORDC15N-NCoA1257-385/STAT6783-81490% H2O/10% D2O
filamentous virus61 mM [U-99% 15N] STAT6, 50 mM HEPES, 150 mM sodium chloride, 10 % D2O, 90% H2O/10% D2ORDC15N-STAT6783-81490% H2O/10% D2O
solution71 mM [U-99% 13C; U-99% 15N] STAT6, 0.7 mM NCoA1, 50 mM HEPES, 150 mM sodium chloride, 100 % D2O, 100% D2OD2O15N,13C- STAT6783-814/NCoA1257-385100% D2O
solution80.7 mM [U-99% 13C; U-99% 15N] NCoA1, 1 mM STAT6, 50 mM HEPES, 150 mM sodium chloride, 100 % D2O, 100% D2OD2O15N,13C NCoA1257-385/STAT6783-814100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMHEPESnatural abundance1
150 mMsodium chloridenatural abundance1
10 %D2Onatural abundance1
1 mMSTAT6[U-99% 13C; U-99% 15N]1
1 mMSTAT6[U-99% 13C; U-99% 15N]2
0.7 mMNCoA1natural abundance2
50 mMHEPESnatural abundance2
150 mMsodium chloridenatural abundance2
10 %D2Onatural abundance2
0.7 mMNCoA1[U-99% 13C; U-99% 15N]3
1 mMSTAT6natural abundance3
50 mMHEPESnatural abundance3
150 mMsodium chloridenatural abundance3
10 %D2Onatural abundance3
1 mMSTAT6[U-99% 15N]4
0.7 mMNCoA1natural abundance4
50 mMHEPESnatural abundance4
150 mMsodium chloridenatural abundance4
10 %D2Onatural abundance4
0.7 mMNCoA1[U-99% 15N]5
1 mMSTAT6natural abundance5
50 mMHEPESnatural abundance5
150 mMsodium chloridenatural abundance5
10 %D2Onatural abundance5
1 mMSTAT6[U-99% 15N]6
50 mMHEPESnatural abundance6
150 mMsodium chloridenatural abundance6
10 %D2Onatural abundance6
1 mMSTAT6[U-99% 13C; U-99% 15N]7
0.7 mMNCoA1natural abundance7
50 mMHEPESnatural abundance7
150 mMsodium chloridenatural abundance7
100 %D2Onatural abundance7
0.7 mMNCoA1[U-99% 13C; U-99% 15N]8
1 mMSTAT6natural abundance8
50 mMHEPESnatural abundance8
150 mMsodium chloridenatural abundance8
100 %D2Onatural abundance8
Sample conditionsIonic strength: 150 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 309 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001room temperature probe
Bruker AVANCE IIIBrukerAVANCE III7002room temperature probe
Bruker AVANCE IIIBrukerAVANCE III6003cryoprobe
Bruker AVANCE IIIBrukerAVANCE III7004cryoprobe
Bruker AVANCE IIIBrukerAVANCE III8005cryoprobe
Bruker AVANCE IIIBrukerAVANCE III9006cryoprobe

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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