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- PDB-6g0h: BRD4 (BD1) in complex with APSC-derived ligands (e.g. SSLH01 a su... -

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Basic information

Entry
Database: PDB / ID: 6g0h
TitleBRD4 (BD1) in complex with APSC-derived ligands (e.g. SSLH01 a sulfasalazine derivate)
ComponentsBromodomain-containing protein 4
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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / 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 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EGE / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.907 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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)15,6534
Polymers15,0991
Non-polymers5543
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.426, 108.102, 30.219
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Detailsbiological unit is the same as asym.

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Components

#1: Protein Bromodomain-containing protein 4 / 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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-EGE / 4-azanyl-2-oxidanyl-5-[(~{E})-[4-(pyridin-2-ylsulfamoyl)phenyl]diazenyl]benzoic acid


Mass: 413.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15N5O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.1 Å3/Da / Density % sol: 42 % / Mosaicity: 0.102 °
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: 1.7699 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: 1.7699 Å / Relative weight: 1
ReflectionResolution: 1.907→37.039 Å / Num. obs: 9903 / % possible obs: 93.3 % / Observed criterion σ(I): -3 / Redundancy: 8.484 % / Biso Wilson estimate: 27.871 Å2 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.088 / Net I/σ(I): 22.49
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allDiffraction-ID% possible all
1.91-1.960.5442.885100.583168.2
1.96-2.010.4743.966490.501185.1
2.01-2.070.4135.346590.432191.7
2.07-2.140.3376.776420.353192.6
2.14-2.210.2378.626460.249193.5
2.21-2.280.20810.856330.218195.5
2.28-2.370.18712.126140.195195
2.37-2.470.16713.595900.175195.6
2.47-2.580.14616.575740.153195.8
2.58-2.70.1319.975420.135196.4
2.7-2.850.1123.445320.115196.9
2.85-3.020.09228.255250.096197.6
3.02-3.230.07633.54590.079197.9
3.23-3.490.0640.854580.063198.1
3.49-3.820.05248.634360.054199.1
3.82-4.270.04455.373790.046198.7
4.27-4.930.04356.723520.045199.4
4.93-6.040.04551.72950.046199.3
6.04-8.540.04154.812390.0431100
8.54-37.0390.03168.011520.033199.3

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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
PHASER2.7.17phasing
PDB_EXTRACT3.11data extraction
XSCALE1.11.2016data scaling
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.907→37.039 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.226 908 5 %
Rwork0.1844 --
obs0.1866 9899 93.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.45 Å2 / Biso mean: 26.4849 Å2 / Biso min: 10.73 Å2
Refinement stepCycle: LAST / Resolution: 1.907→37.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 37 86 1185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9067-2.02620.34331210.2832346246777
2.0262-2.18260.2661500.23072877302793
2.1826-2.40220.23971510.20482951310295
2.4022-2.74970.23631540.19133004315897
2.7497-3.4640.22621630.17522991315498
3.464-37.04650.1921690.156130793248100

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