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- PDB-5u5s: Solution structures of Brd2 second bromodomain in complex with st... -

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Basic information

Entry
Database: PDB / ID: 5u5s
TitleSolution structures of Brd2 second bromodomain in complex with stat3 peptide
Components
  • Bromodomain-containing protein 2BRD2
  • Stat3 peptide
KeywordsTRANSCRIPTION / Brd2 / Brd4 / bromodomain / stat3 / th17 / p300
Function / homology
Function and homology information


RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / retinal rod cell differentiation / radial glial cell differentiation / cell surface receptor signaling pathway via STAT / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / negative regulation of neuron migration ...RNA sequestering activity / positive regulation of metalloendopeptidase activity / PTK6 Activates STAT3 / eye photoreceptor cell differentiation / retinal rod cell differentiation / radial glial cell differentiation / cell surface receptor signaling pathway via STAT / negative regulation of primary miRNA processing / leptin-mediated signaling pathway / negative regulation of neuron migration / T-helper 17 type immune response / Signalling to STAT3 / negative regulation of inflammatory response to wounding / primary miRNA binding / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / response to leptin / regulation of feeding behavior / sexual reproduction / interleukin-11-mediated signaling pathway / T-helper 17 cell lineage commitment / cellular response to interleukin-17 / Transcriptional regulation of pluripotent stem cells / Interleukin-9 signaling / Interleukin-21 signaling / interleukin-9-mediated signaling pathway / MET activates STAT3 / interleukin-2-mediated signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / intracellular receptor signaling pathway / chromatin looping / STAT3 nuclear events downstream of ALK signaling / negative regulation of stem cell differentiation / acetylation-dependent protein binding / interleukin-15-mediated signaling pathway / cellular response to leptin stimulus / positive regulation of cytokine production involved in inflammatory response / astrocyte differentiation / Interleukin-23 signaling / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-37 signaling / Interleukin-15 signaling / Signaling by Leptin / Interleukin-35 Signalling / Interleukin-27 signaling / negative regulation of glycolytic process / positive regulation of vascular endothelial cell proliferation / growth hormone receptor signaling pathway / temperature homeostasis / eating behavior / Signaling by ALK / Interleukin-20 family signaling / Interleukin-6 signaling / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / Association of TriC/CCT with target proteins during biosynthesis / somatic stem cell population maintenance / Interleukin-10 signaling / cell surface receptor signaling pathway via JAK-STAT / positive regulation of interleukin-10 production / RUNX3 regulates p14-ARF / Signaling by ALK fusions and activated point mutants / regulation of multicellular organism growth / positive regulation of vascular endothelial growth factor production / positive regulation of T-helper 17 cell lineage commitment / growth hormone receptor signaling pathway via JAK-STAT / Nuclear events stimulated by ALK signaling in cancer / signaling adaptor activity / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / energy homeostasis / Growth hormone receptor signaling / Signaling by CSF3 (G-CSF) / cellular response to hormone stimulus / protein localization to chromatin / Interleukin-7 signaling / Downstream signal transduction / negative regulation of autophagy / transforming growth factor beta receptor signaling pathway / positive regulation of erythrocyte differentiation / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of interleukin-1 beta production / neural tube closure / positive regulation of interleukin-8 production / lysine-acetylated histone binding / PKR-mediated signaling / mRNA transcription by RNA polymerase II / defense response / Inactivation of CSF3 (G-CSF) signaling / Signaling by SCF-KIT / Cytoprotection by HMOX1 / chromatin DNA binding / response to peptide hormone / negative regulation of inflammatory response / nucleosome assembly / positive regulation of miRNA transcription / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / protein import into nucleus / Transcriptional regulation of granulopoiesis
Similarity search - Function
STAT3, SH2 domain / : / Signal transducer and activator of transcription, linker 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 ...STAT3, SH2 domain / : / Signal transducer and activator of transcription, linker 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 / p53-like transcription factor, DNA-binding / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / SH2 domain / Src homology 2 (SH2) domain profile. / SH2 domain / SH2 domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 2 / Signal transducer and activator of transcription 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZeng, L. / Zhou, M.-M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Mol. Cell / Year: 2017
Title: Distinct Roles of Brd2 and Brd4 in Potentiating the Transcriptional Program for Th17 Cell Differentiation.
Authors: Cheung, K.L. / Zhang, F. / Jaganathan, A. / Sharma, R. / Zhang, Q. / Konuma, T. / Shen, T. / Lee, J.Y. / Ren, C. / Chen, C.H. / Lu, G. / Olson, M.R. / Zhang, W. / Kaplan, M.H. / Littman, D.R. ...Authors: Cheung, K.L. / Zhang, F. / Jaganathan, A. / Sharma, R. / Zhang, Q. / Konuma, T. / Shen, T. / Lee, J.Y. / Ren, C. / Chen, C.H. / Lu, G. / Olson, M.R. / Zhang, W. / Kaplan, M.H. / Littman, D.R. / Walsh, M.J. / Xiong, H. / Zeng, L. / Zhou, M.M.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_exptl ...pdbx_audit_support / pdbx_nmr_exptl / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_exptl.type / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Stat3 peptide


Theoretical massNumber of molelcules
Total (without water)14,6982
Polymers14,6982
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13157.136 Da / Num. of mol.: 1 / Fragment: UNP residues 344-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Protein/peptide Stat3 peptide


Mass: 1540.808 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P40763*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic13D HN(CA)CB
122isotropic13D HN(COCA)CB
132isotropic23D 1H-15N NOESY
141isotropic33D 1H-13C NOESY aliphatic
151isotropic33D 1H-13C NOESY aromatic
161isotropic23D 1H-13C filtered NOESY aliphatic
171isotropic23D 1H-13C filtered NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 100% D2Osample_1100% D2O
solution210 mM sodium phosphate, 100 mM sodium chloride, 2 mM EDTA, 2 mM [U-2H] DTT, 90% H2O/10% D2Osample_290% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
2 mMEDTAnatural abundance1
2 mMDTT[U-2H]1
10 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
2 mMEDTAnatural abundance2
2 mMDTT[U-2H]2
Sample conditionsIonic strength: null Not defined / Label: conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE9003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
NMRView5.04Johnson, One Moon Scientificpeak picking
TALOSCornilescu, Delaglio and Baxrefinement
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProcheckNMRLaskowski and MacArthurdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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