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- PDB-2lsp: solution structures of BRD4 second bromodomain with NF-kB-K310ac ... -

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Basic information

Entry
Database: PDB / ID: 2lsp
Titlesolution structures of BRD4 second bromodomain with NF-kB-K310ac peptide
Components
  • Bromodomain-containing protein 4BRD4
  • NF-kB-K310ac peptide
KeywordsPROTEIN BINDING / NF-kB / BRD4 / HIV / bromodomain / kidney disease
Function / homology
Function and homology information


acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 ...acetaldehyde metabolic process / prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / negative regulation of non-canonical NF-kappaB signal transduction / NF-kappaB complex / cellular response to angiotensin / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / RNA polymerase II C-terminal domain binding / The NLRP3 inflammasome / negative regulation of DNA damage checkpoint / general transcription initiation factor binding / Transcriptional Regulation by VENTX / P-TEFb complex binding / NF-kappaB binding / hair follicle development / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / positive regulation of T-helper 17 cell lineage commitment / cellular response to interleukin-1 / cellular defense response / Purinergic signaling in leishmaniasis infection / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / response to muscle stretch / histone reader activity / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / response to interleukin-1 / negative regulation of angiogenesis / RNA polymerase II CTD heptapeptide repeat kinase activity / negative regulation of miRNA transcription / liver development / response to progesterone / condensed nuclear chromosome / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / Activation of NF-kappaB in B cells / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / protein catabolic process / TAK1-dependent IKK and NF-kappa-B activation / lysine-acetylated histone binding / response to insulin / transcription coactivator binding / negative regulation of protein catabolic process / chromatin DNA binding / cellular response to hydrogen peroxide / PKMTs methylate histone lysines / CLEC7A (Dectin-1) signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Interleukin-1 signaling
Similarity search - Function
Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. ...Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
Homo Sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing, torsion angle dynamics
AuthorsZhang, G. / Liu, R. / Zhong, Y. / Plotnikov, A.N. / Zhang, W. / Rusinova, E. / Gerona-Nevarro, G. / Moshkina, N. / Joshua, J. / Chuang, P.Y. ...Zhang, G. / Liu, R. / Zhong, Y. / Plotnikov, A.N. / Zhang, W. / Rusinova, E. / Gerona-Nevarro, G. / Moshkina, N. / Joshua, J. / Chuang, P.Y. / Ohlmeyer, M. / He, J. / Zhou, M.-M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Down-regulation of NF-kappa B transcriptional activity in HIV-associated kidney disease by BRD4 inhibition.
Authors: Zhang, G. / Liu, R. / Zhong, Y. / Plotnikov, A.N. / Zhang, W. / Zeng, L. / Rusinova, E. / Gerona-Nevarro, G. / Moshkina, N. / Joshua, J. / Chuang, P.Y. / Ohlmeyer, M. / He, J.C. / Zhou, M.M.
History
DepositionMay 3, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / struct_conn
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 / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NF-kB-K310ac peptide
B: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)16,5062
Polymers16,5062
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide NF-kB-K310ac peptide


Mass: 1663.956 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo Sapiens (human) / References: UniProt: Q04206
#2: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 14842.058 Da / Num. of mol.: 1 / Fragment: second bromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60885

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D HN(CA)CB
1223D HN(COCA)CB
1323D 1H-15N NOESY
1413D 1H-13C NOESY aliphatic
1513D 1H-13C NOESY aromatic
1613D 13C-Edited-15N/13C filtered NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 100% D2O100% D2O
2100 mM sodium phosphate, 5 mM [U-100% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium phosphate-11
5 mMDTT-2[U-100% 2H]1
100 mMsodium phosphate-32
5 mMDTT-4[U-100% 2H]2
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE6003
Bruker DRXBrukerDRX5004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
TALOS3.70F1Cornilescu, Delaglio and Baxgeometry optimization
NMRView5.04Johnson, One Moon Scientificchemical shift assignment
NMRView5.04Johnson, One Moon Scientificdata analysis
NMRView5.04Johnson, One Moon Scientificpeak picking
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: DGSA-distance geometry simulated annealing, 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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