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- PDB-6bnh: Solution NMR structures of BRD4 ET domain with JMJD6 peptide -

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Basic information

Entry
Database: PDB / ID: 6bnh
TitleSolution NMR structures of BRD4 ET domain with JMJD6 peptide
Components
  • Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
  • Bromodomain-containing protein 4
KeywordsTRANSCRIPTION/OXIDOREDUCTASE / RNA / BET / Complex / TRANSCRIPTION-OXIDOREDUCTASE complex
Function / homology
Function and homology information


peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / oxidative RNA demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor ...peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine / histone H3R2 demethylase activity / peptidyl-lysine 5-dioxygenase activity / histone H4R3 demethylase activity / protein demethylase activity / recognition of apoptotic cell / negative regulation of protein homooligomerization / oxidative RNA demethylation / oxidative RNA demethylase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / macrophage activation / non-membrane-bounded organelle assembly / transcription regulator activator activity / regulation of mRNA splicing, via spliceosome / sprouting angiogenesis / Protein hydroxylation / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone demethylase activity / negative regulation by host of viral transcription / erythrocyte development / positive regulation of T-helper 17 cell lineage commitment / phagocytosis / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / RNA splicing / condensed nuclear chromosome / kidney development / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lung development / lysine-acetylated histone binding / HDMs demethylate histones / protein homooligomerization / mRNA processing / p53 binding / retina development in camera-type eye / chromosome / signaling receptor activity / heart development / regulation of inflammatory response / T cell differentiation in thymus / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / single-stranded RNA binding / cell surface receptor signaling pathway / transcription cis-regulatory region binding / chromatin remodeling / ribonucleoprotein complex / iron ion binding / DNA damage response / chromatin binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / NET domain superfamily / NET domain profile. ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #220 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / 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 4 / Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKonuma, T. / Yu, D. / Zhao, C. / Ju, Y. / Sharma, R. / Ren, C. / Zhang, Q. / Zhou, M.-M. / Zeng, L.
CitationJournal: Sci Rep / Year: 2017
Title: Structural Mechanism of the Oxygenase JMJD6 Recognition by the Extraterminal (ET) Domain of BRD4.
Authors: Konuma, T. / Yu, D. / Zhao, C. / Ju, Y. / Sharma, R. / Ren, C. / Zhang, Q. / Zhou, M.M. / Zeng, L.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6


Theoretical massNumber of molelcules
Total (without water)11,5422
Polymers11,5422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1460 Å2
ΔGint-7 kcal/mol
Surface area6540 Å2
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 4 / Protein HUNK1


Mass: 9745.136 Da / Num. of mol.: 1 / Fragment: ET domain residues 601-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Protein/peptide Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 / Histone arginine demethylase JMJD6 / JmjC domain-containing protein 6 / Jumonji domain-containing ...Histone arginine demethylase JMJD6 / JmjC domain-containing protein 6 / Jumonji domain-containing protein 6 / Lysyl-hydroxylase JMJD6 / Peptide-lysine 5-dioxygenase JMJD6 / Phosphatidylserine receptor / Protein PTDSR


Mass: 1797.156 Da / Num. of mol.: 1 / Fragment: residues 84-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD6, KIAA0585, PTDSR / Production host: Escherichia coli (E. coli)
References: UniProt: Q6NYC1, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic32D 1H-15N HSQC
121isotropic33D HN(CA)CB
131isotropic33D CBCA(CO)NH
141isotropic23D 1H-15N NOESY
152isotropic13D 1H-13C NOESY aliphatic
162isotropic13D 1H-13C NOESY aromatic
172isotropic13D filtered 1H-13C NOESY aliphatic
182isotropic13D filtered 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 95% H2O/5% D2O13C_15N_sample195% H2O/5% D2O
solution210 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O13C_15N_sample2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
2 mMDTT[U-100% 2H]1
10 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
2 mMDTT[U-100% 2H]2
Sample conditionsIonic strength units: Not defined / Label: sample_conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ProcheckNMRLaskowski and MacArthurdata analysis
TopSpinBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
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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