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- PDB-6swn: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD1 (GSK778) -

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Basic information

Entry
Database: PDB / ID: 6swn
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH iBET-BD1 (GSK778)
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST
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 / 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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase 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 II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
GLUTAMIC ACID / Chem-LWB / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsChung, C.
CitationJournal: Science / Year: 2020
Title: Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammation.
Authors: Gilan, O. / Rioja, I. / Knezevic, K. / Bell, M.J. / Yeung, M.M. / Harker, N.R. / Lam, E.Y.N. / Chung, C.W. / Bamborough, P. / Petretich, M. / Urh, M. / Atkinson, S.J. / Bassil, A.K. / ...Authors: Gilan, O. / Rioja, I. / Knezevic, K. / Bell, M.J. / Yeung, M.M. / Harker, N.R. / Lam, E.Y.N. / Chung, C.W. / Bamborough, P. / Petretich, M. / Urh, M. / Atkinson, S.J. / Bassil, A.K. / Roberts, E.J. / Vassiliadis, D. / Burr, M.L. / Preston, A.G.S. / Wellaway, C. / Werner, T. / Gray, J.R. / Michon, A.M. / Gobbetti, T. / Kumar, V. / Soden, P.E. / Haynes, A. / Vappiani, J. / Tough, D.F. / Taylor, S. / Dawson, S.J. / Bantscheff, M. / Lindon, M. / Drewes, G. / Demont, E.H. / Daniels, D.L. / Grandi, P. / Prinjha, R.K. / Dawson, M.A.
History
DepositionSep 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8204
Polymers15,0991
Non-polymers7213
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint3 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.280, 42.320, 90.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15099.380 Da / Num. of mol.: 1
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: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-LWB / 4-[2-(methoxymethyl)-1-[(1~{R})-1-phenylethyl]-8-[[(3~{S})-pyrrolidin-3-yl]methoxy]imidazo[4,5-c]quinolin-7-yl]-3,5-dimethyl-1,2-oxazole


Mass: 511.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H33N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG3350, 0.2M NaI, 0.1M BTP, 20C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07253 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07253 Å / Relative weight: 1
ReflectionResolution: 1.28→45.41 Å / Num. obs: 36156 / % possible obs: 93.3 % / Redundancy: 5.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.0365 / Net I/σ(I): 17
Reflection shellResolution: 1.28→1.33 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.187 / Num. unique obs: 2233 / CC1/2: 0.901 / % possible all: 60.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→38.36 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.886 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.059
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2122 1801 4.99 %
Rwork0.1926 --
all0.194 --
obs-36093 93.033 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.298 Å20 Å20 Å2
2--0.055 Å20 Å2
3----0.353 Å2
Refinement stepCycle: LAST / Resolution: 1.28→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 51 270 1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131267
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171172
X-RAY DIFFRACTIONr_angle_refined_deg1.1381.6691744
X-RAY DIFFRACTIONr_angle_other_deg1.1591.6532751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4165147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71224.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78915221
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.888154
X-RAY DIFFRACTIONr_chiral_restr0.0560.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02242
X-RAY DIFFRACTIONr_nbd_refined0.1880.2265
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.2984
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2185
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1190.216
X-RAY DIFFRACTIONr_nbd_other0.1660.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.223
X-RAY DIFFRACTIONr_mcbond_it0.7521.979544
X-RAY DIFFRACTIONr_mcbond_other0.7521.972543
X-RAY DIFFRACTIONr_mcangle_it1.2844.429689
X-RAY DIFFRACTIONr_mcangle_other1.2834.442690
X-RAY DIFFRACTIONr_scbond_it1.1032.152723
X-RAY DIFFRACTIONr_scbond_other1.1022.151724
X-RAY DIFFRACTIONr_scangle_it1.8054.741049
X-RAY DIFFRACTIONr_scangle_other1.8044.741050
X-RAY DIFFRACTIONr_lrange_it5.08819.6061712
X-RAY DIFFRACTIONr_lrange_other4.54617.9061621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.28-1.3140.307740.27214920.27328060.860.87255.8090.249
1.314-1.350.259880.24419500.24427540.8930.90474.00150.222
1.35-1.3890.2681180.23821190.23926890.9120.90683.19080.213
1.389-1.4310.261040.21622980.21825930.9110.92292.6340.196
1.431-1.4780.2551190.21423880.21625250.9220.92799.28710.194
1.478-1.530.2231230.2123200.21124490.9330.93899.7550.199
1.53-1.5880.2461160.20922530.21123730.9210.93399.83140.201
1.588-1.6520.2141280.19921350.222690.9390.94199.73560.193
1.652-1.7260.2671320.20120550.20521920.9150.9499.77190.202
1.726-1.810.2091070.19319740.19420840.9450.94799.8560.199
1.81-1.9070.218950.18919290.19120250.9350.94699.95060.201
1.907-2.0230.194860.1918010.1919050.9540.95399.05510.208
2.023-2.1620.188800.17816820.17917690.9570.95899.60430.203
2.162-2.3350.209710.17216030.17416770.9530.96199.82110.199
2.335-2.5560.202840.17914670.1815590.9530.95699.48690.213
2.556-2.8570.235710.18813260.1914020.9330.94899.64340.23
2.857-3.2950.173910.17411630.17412580.960.96199.6820.214
3.295-4.0290.183500.17810240.17810810.9540.95999.35240.216
4.029-5.6660.195440.1878130.1878610.9520.95599.53540.23
5.666-38.360.275200.255000.2515240.9260.91799.23660.288

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