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- PDB-4kv1: Crystal Structure of Brd4 Bromodomain 1 in Complex with Acetylate... -

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Basic information

Entry
Database: PDB / ID: 4kv1
TitleCrystal Structure of Brd4 Bromodomain 1 in Complex with Acetylated Rel Peptide
Components
  • Bromodomain-containing protein 4BRD4
  • Rel peptide
KeywordsTRANSCRIPTION / Rel / P65 / Bromodomain
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
C: Rel peptide
B: Bromodomain-containing protein 4
D: Rel peptide


Theoretical massNumber of molelcules
Total (without water)32,1354
Polymers32,1354
Non-polymers00
Water5,549308
1
A: Bromodomain-containing protein 4
C: Rel peptide


Theoretical massNumber of molelcules
Total (without water)16,0682
Polymers16,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-8 kcal/mol
Surface area7900 Å2
MethodPISA
2
B: Bromodomain-containing protein 4
D: Rel peptide


Theoretical massNumber of molelcules
Total (without water)16,0682
Polymers16,0682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-9 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.011, 59.733, 118.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 15170.456 Da / Num. of mol.: 2 / Fragment: UNP residues 41-168
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.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG 3350, 0.2 M NaNO3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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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: 1.5→50 Å / Num. obs: 48227 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.55 Å / % possible all: 89

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→34.363 Å / SU ML: 0.33 / σ(F): 1.34 / Phase error: 21.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2223 2429 5.04 %
Rwork0.198 --
obs0.1992 48157 98.73 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.856 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1092 Å2-0 Å2-0 Å2
2---1.9223 Å2-0 Å2
3----2.1869 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 0 308 2552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062310
X-RAY DIFFRACTIONf_angle_d1.0373138
X-RAY DIFFRACTIONf_dihedral_angle_d11.989901
X-RAY DIFFRACTIONf_chiral_restr0.07336
X-RAY DIFFRACTIONf_plane_restr0.005400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53050.26131250.22072294X-RAY DIFFRACTION87
1.5305-1.56380.23731350.20932517X-RAY DIFFRACTION94
1.5638-1.60020.24741280.19462656X-RAY DIFFRACTION99
1.6002-1.64020.21631430.18732698X-RAY DIFFRACTION100
1.6402-1.68450.22541350.19162700X-RAY DIFFRACTION100
1.6845-1.73410.23691490.18952675X-RAY DIFFRACTION100
1.7341-1.79010.22331310.19922713X-RAY DIFFRACTION100
1.7901-1.85410.23161400.19252686X-RAY DIFFRACTION100
1.8541-1.92830.22161520.19162716X-RAY DIFFRACTION100
1.9283-2.0160.23571590.19482688X-RAY DIFFRACTION100
2.016-2.12230.22861490.1932707X-RAY DIFFRACTION100
2.1223-2.25520.21621490.19252720X-RAY DIFFRACTION100
2.2552-2.42930.23491370.19872736X-RAY DIFFRACTION100
2.4293-2.67370.23571520.20712749X-RAY DIFFRACTION100
2.6737-3.06040.2481590.20472746X-RAY DIFFRACTION100
3.0604-3.8550.22161380.19162818X-RAY DIFFRACTION100
3.855-34.37220.18071480.20342909X-RAY DIFFRACTION99

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