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- PDB-4kv4: Brd4 Bromodomain 2 in Complex with Acetylated Rel Peptide -

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Basic information

Entry
Database: PDB / ID: 4kv4
TitleBrd4 Bromodomain 2 in Complex with Acetylated Rel Peptide
Components
  • Bromodomain-containing protein 4
  • Rel Peptide
KeywordsTRANSCRIPTION / Rel / P65 / Bromodomain
Function / homology
Function and homology information


prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / ankyrin repeat binding / Regulated proteolysis of p75NTR / CLEC7A/inflammasome pathway ...prolactin signaling pathway / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / toll-like receptor TLR6:TLR2 signaling pathway / IkBA variant leads to EDA-ID / positive regulation of Schwann cell differentiation / cellular response to peptidoglycan / ankyrin repeat binding / Regulated proteolysis of p75NTR / CLEC7A/inflammasome pathway / SUMOylation of immune response proteins / RIP-mediated NFkB activation via ZBP1 / postsynapse to nucleus signaling pathway / negative regulation of protein sumoylation / Interleukin-1 processing / nucleotide-binding oligomerization domain containing 2 signaling pathway / defense response to tumor cell / cellular response to interleukin-6 / actinin binding / response to UV-B / non-canonical NF-kappaB signal transduction / negative regulation of non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / interleukin-1-mediated signaling pathway / signal transduction involved in regulation of gene expression / NF-kappaB complex / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / response to cobalamin / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / RNA polymerase II C-terminal domain binding / TRAF6 mediated NF-kB activation / P-TEFb complex binding / negative regulation of DNA damage checkpoint / positive regulation of vascular endothelial growth factor production / Transcriptional Regulation by VENTX / cellular response to angiotensin / The NLRP3 inflammasome / histone H4 reader activity / general transcription initiation factor binding / cellular response to interleukin-1 / host-mediated suppression of viral transcription / hair follicle development / canonical NF-kappaB signal transduction / neuropeptide signaling pathway / NF-kappaB binding / response to amino acid / cellular defense response / positive regulation of T-helper 17 cell lineage commitment / RNA polymerase II core promoter sequence-specific DNA binding / Purinergic signaling in leishmaniasis infection / response to cAMP / NF-kB is activated and signals survival / tumor necrosis factor-mediated signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / response to muscle stretch / response to cytokine / positive regulation of interleukin-12 production / antiviral innate immune response / peptide binding / negative regulation of cytokine production involved in inflammatory response / RNA polymerase II CTD heptapeptide repeat kinase activity / CD209 (DC-SIGN) signaling / : / response to interleukin-1 / negative regulation of insulin receptor signaling pathway / negative regulation of miRNA transcription / response to progesterone / negative regulation of angiogenesis / Dectin-1 mediated noncanonical NF-kB signaling / condensed nuclear chromosome / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / animal organ morphogenesis / positive regulation of interleukin-1 beta production / Activation of NF-kappaB in B cells / response to ischemia / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of interleukin-8 production / TAK1-dependent IKK and NF-kappa-B activation / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of transcription elongation by RNA polymerase II / chromatin DNA binding / protein catabolic process / liver development / positive regulation of non-canonical NF-kappaB signal transduction / CLEC7A (Dectin-1) signaling / positive regulation of NF-kappaB transcription factor activity / negative regulation of protein catabolic process / response to insulin / FCERI mediated NF-kB activation / Interleukin-1 signaling / PKMTs methylate histone lysines
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 / 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 / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Bromodomain-containing protein 4 / Transcription factor p65
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, H. / Nair, S.K.
CitationJournal: Oncogene / Year: 2014
Title: Brd4 maintains constitutively active NF-kappa B in cancer cells by binding to acetylated RelA.
Authors: Zou, Z. / Huang, B. / Wu, X. / Zhang, H. / Qi, J. / Bradner, J. / Nair, S. / Chen, L.F.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Rel Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9293
Polymers13,7752
Non-polymers1541
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-8 kcal/mol
Surface area7200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.026, 73.599, 33.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 12877.922 Da / Num. of mol.: 1 / Fragment: UNP residues 351-459
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 Rel Peptide


Mass: 897.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE REL PEPTIDE CORRESPONDS TO RESIDUES THR308-LYS314 OF NF-KAPPA B (WITH LYS210 ACETYLATED).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.5 M (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 9987 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHARPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→30.585 Å / SU ML: 0.5 / σ(F): 1.34 / Phase error: 25.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2578 478 4.8 %
Rwork0.2078 --
obs0.2102 9955 98.92 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.598 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1446 Å20 Å2-0 Å2
2--0.5357 Å2-0 Å2
3----0.6803 Å2
Refinement stepCycle: LAST / Resolution: 2→30.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 8 57 1007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011973
X-RAY DIFFRACTIONf_angle_d1.0411302
X-RAY DIFFRACTIONf_dihedral_angle_d15.665368
X-RAY DIFFRACTIONf_chiral_restr0.074134
X-RAY DIFFRACTIONf_plane_restr0.004165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.28940.31371290.22233050X-RAY DIFFRACTION97
2.2894-2.88410.30321750.21653130X-RAY DIFFRACTION100
2.8841-30.58860.23051740.20143297X-RAY DIFFRACTION100

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