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- PDB-2l5e: Complex between BD1 of Brd3 and GATA-1 C-tail -

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Basic information

Entry
Database: PDB / ID: 2l5e
TitleComplex between BD1 of Brd3 and GATA-1 C-tail
Components
  • Bromodomain-containing protein 3
  • GATA-1
KeywordsNUCLEAR PROTEIN/TRANSCRIPTION / GATA-1 / Brd3 / histone code / NUCLEAR PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / myeloid cell apoptotic process / primitive erythrocyte differentiation / megakaryocyte differentiation / osteoblast proliferation / cell development ...regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / myeloid cell apoptotic process / primitive erythrocyte differentiation / megakaryocyte differentiation / osteoblast proliferation / cell development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Sertoli cell development / dendritic cell differentiation / negative regulation of bone mineralization / Factors involved in megakaryocyte development and platelet production / cellular response to follicle-stimulating hormone stimulus / positive regulation of mast cell degranulation / negative regulation of myeloid cell apoptotic process / myeloid cell differentiation / C2H2 zinc finger domain binding / DNA binding, bending / embryonic hemopoiesis / platelet formation / lncRNA binding / bone mineralization / positive regulation of osteoblast proliferation / endodermal cell differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / animal organ regeneration / erythrocyte development / cis-regulatory region sequence-specific DNA binding / protein localization to chromatin / homeostasis of number of cells within a tissue / cellular response to cAMP / transcription repressor complex / erythrocyte differentiation / positive regulation of erythrocyte differentiation / transcription coregulator binding / : / molecular condensate scaffold activity / transcription coactivator binding / protein-DNA complex / chromatin DNA binding / platelet aggregation / p53 binding / cell-cell signaling / chromatin organization / cellular response to lipopolysaccharide / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / in utero embryonic development / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. ...Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, NHR/GATA-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Erythroid transcription factor / Bromodomain-containing protein 3 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsGamsjaeger, R. / Webb, S.R. / Lamonica, J.M. / Blobel, G.A. / Mackay, J.P.
CitationJournal: Mol. Cell. Biol. / Year: 2011
Title: Structural basis and specificity of acetylated transcription factor GATA1 recognition by BET family bromodomain protein Brd3.
Authors: Gamsjaeger, R. / Webb, S.R. / Lamonica, J.M. / Billin, A. / Blobel, G.A. / Mackay, J.P.
History
DepositionOct 31, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model ..._pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 30, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: GATA-1


Theoretical massNumber of molelcules
Total (without water)16,4582
Polymers16,4582
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Bromodomain-containing protein 3 / Bromodomain containing 3 / isoform CRA_d


Mass: 15024.313 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brd3, mCG_11349, RP23-328F3.1-001 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3TUI3, UniProt: Q8K2F0*PLUS
#2: Protein/peptide GATA-1


Mass: 1433.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P17679*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCO
1613D HN(CO)CA
1713D HBHA(CO)NH
1812D 1H-15N HSQC
1923D (H)CCH-TOCSY
11023D (H)CCH-TOCSY
11113D HNHA
11213D HCC(CO)NH TOCSY
11313D CC(CO)NH TOCSY
11413D 13C sep (F2) 15N13C filtered (F1) NOESY
11513D 13C sep (F1) 15N13C filtered (F3) NOESY
11612D 15N13C filtered NOESY
11712D 15N13C filtered TOCSY
11823D 13C NOESY
11913D 15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.5 mM [U-13C; U-15N] entity_1-1, 0.5-1.5 mM entity_2-2, 100 mM NaCl-3, 20 mM Tris-4, 1 mM DTT-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5-1.5 mM [U-13C; U-15N] entity_1-6, 0.5-1.5 mM entity_2-7, 100 mM NaCl-8, 20 mM Tris-9, 1 mM DTT-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity_1-1[U-13C; U-15N]0.5-1.51
mMentity_2-20.5-1.51
100 mMNaCl-31
20 mMTris-41
1 mMDTT-51
mMentity_1-6[U-13C; U-15N]0.5-1.52
mMentity_2-70.5-1.52
100 mMNaCl-82
20 mMTris-92
1 mMDTT-102
Sample conditionspH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionClassification
CNS1.1chemical shift assignment
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: CNS/ARIA1.2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Representative conformer: 1

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