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- PDB-6g0g: BRD4 (BD1) in complex with APSC-derived ligands (e.g. sulfasalazine) -

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Basic information

Entry
Database: PDB / ID: 6g0g
TitleBRD4 (BD1) in complex with APSC-derived ligands (e.g. sulfasalazine)
ComponentsBromodomain-containing protein 4BRD4
KeywordsTRANSCRIPTION / BRD4
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / Chem-SAS / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.478 Å
AuthorsHumbeck, L. / Pretzel, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSPP 1736 Germany
German Federal Ministry for Education and Research (BMBF)BMBF Grant 1316053 Germany
CitationJournal: Chemrxiv / Year: 2019
Title: Discovery of an Unexpected Similarity in Ligand Binding Between BRD4 and PPARgamma
Authors: Humbeck, L. / Pretzel, J. / Spitzer, S. / Koch, O.
History
DepositionMar 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6845
Polymers15,0991
Non-polymers5854
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint4 kcal/mol
Surface area7890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.322, 108.176, 30.227
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: BD1 / Mutation: T43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885

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Non-polymers , 5 types, 127 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-SAS / 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID / SULFASALAZINE / Sulfasalazine


Mass: 398.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14N4O5S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 42.7 % / Mosaicity: 0.077 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate anhydrous pH 4.6 and 3.5 M sodium formate, cryo protection: 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.478→36.956 Å / Num. obs: 22364 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.99 % / Biso Wilson estimate: 24.93 Å2 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.079 / Net I/σ(I): 19.61
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allDiffraction-ID% possible all
1.49-1.530.8932.2415990.932199.9
1.53-1.570.7912.5815530.8271100
1.57-1.620.6823.1814890.711100
1.62-1.670.5694.0214740.5921100
1.67-1.720.4744.8114300.4941100
1.72-1.780.4055.8213770.421199.9
1.78-1.850.3167.6613040.329199.9
1.85-1.920.2419.7112820.252199.9
1.92-2.010.1912.7912470.1981100
2.01-2.110.15716.8211770.1631100
2.11-2.220.1221.411270.1251100
2.22-2.360.11323.7410870.1171100
2.36-2.520.09527.6710030.098199.9
2.52-2.720.07731.749400.081100
2.72-2.980.0641.228770.0621100
2.98-3.330.04651.678090.0481100
3.33-3.850.03466.897150.0361100
3.85-4.710.02876.566020.0291100
4.71-6.660.02866.874980.031100
6.66-36.9560.02384.472970.024199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
PHENIX1.13rc1-2961refinement
XDS1.11.2016data reduction
PHASER2.6.1phasing
PDB_EXTRACT3.11data extraction
XSCALE1.11.2016data scaling
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.478→36.956 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.95
RfactorNum. reflection% reflection
Rfree0.2195 1116 4.99 %
Rwork0.1928 --
obs0.1942 22356 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.74 Å2 / Biso mean: 23.4171 Å2 / Biso min: 11.21 Å2
Refinement stepCycle: LAST / Resolution: 1.478→36.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 39 123 1208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4784-1.54570.29121370.24282584272199
1.5457-1.62720.26341350.223526022737100
1.6272-1.72910.24481350.213125972732100
1.7291-1.86260.2421390.213726342773100
1.8626-2.05010.24681390.195426462785100
2.0501-2.34670.23971400.185926642804100
2.3467-2.95640.211410.195926762817100
2.9564-36.96770.1961500.180328372987100

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