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- PDB-6djc: Crystal structure of human Bromodomain-containing protein 4 (BRD4... -

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Basic information

Entry
Database: PDB / ID: 6djc
TitleCrystal structure of human Bromodomain-containing protein 4 (BRD4) bromodomain with MS645
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION/INHIBITOR / transcription / inhibitor / histone acetylation / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-CF6 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsRen, C. / Zhou, M.M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Spatially constrained tandem bromodomain inhibition bolsters sustained repression of BRD4 transcriptional activity for TNBC cell growth.
Authors: Ren, C. / Zhang, G. / Han, F. / Fu, S. / Cao, Y. / Zhang, F. / Zhang, Q. / Meslamani, J. / Xu, Y. / Ji, D. / Cao, L. / Zhou, Q. / Cheung, K.L. / Sharma, R. / Babault, N. / Yi, Z. / Zhang, W. ...Authors: Ren, C. / Zhang, G. / Han, F. / Fu, S. / Cao, Y. / Zhang, F. / Zhang, Q. / Meslamani, J. / Xu, Y. / Ji, D. / Cao, L. / Zhou, Q. / Cheung, K.L. / Sharma, R. / Babault, N. / Yi, Z. / Zhang, W. / Walsh, M.J. / Zeng, L. / Zhou, M.M.
History
DepositionMay 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
A: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,80911
Polymers31,3742
Non-polymers1,4359
Water6,305350
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B: Bromodomain-containing protein 4
hetero molecules

A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,80911
Polymers31,3742
Non-polymers1,4359
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)54.000, 59.720, 95.620
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 / Protein HUNK1


Mass: 15687.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: proteolysis during crystallization / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-CF6 / N,N'-(decane-1,10-diyl)bis{2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide}


Mass: 938.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H54Cl2N10O2S2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe complete crystallized sequence was: ...The complete crystallized sequence was: SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMIVQAKGRGRGRKETGTAKPGVSTVPNTTQASTPPQTQTPQPNPPPVQATPHPFPAVTPDLIVQTPVMTVVPPQPLQTPPPVPPQPQPPPAPAPQPVQSHPPIIAATPQPVKTKKGVKRKADTTTPTTIDPIHEPPSLPPEPKTTKLGQRRESSRPVKPPKKDVPDSQQHPAPEKSSKVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPDEPEEPVVAVSSPAVPPPT. Due to undesired cleavage during crystallization, the final sequence present the crystal is: SMNPPPPETSNPNKPKRQTNQLQYLLRVVLKTLWKHQFAWPFQQPVDAVKLNLPDYYKIIKTPMDMGTIKKRLENNYYWNAQECIQDFNTMFTNCYIYNKPGDDIVLMAEALEKLFLQKINELPTEETEIMI (SM is from the tag).

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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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium sulfate, 0.1M Bis-Tris pH6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.08754 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08754 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 50373 / % possible obs: 92.8 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.013 / Net I/σ(I): 53.6
Reflection shellResolution: 1.46→1.49 Å / Rmerge(I) obs: 0.914 / Rpim(I) all: 0.281

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZYU

3zyu


Resolution: 1.46→37.323 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 16.84
RfactorNum. reflection% reflection
Rfree0.1762 2460 4.89 %
Rwork0.141 --
obs0.1427 50320 92.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.46→37.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 96 350 2602
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052324
X-RAY DIFFRACTIONf_angle_d1.4173158
X-RAY DIFFRACTIONf_dihedral_angle_d12.293889
X-RAY DIFFRACTIONf_chiral_restr0.065333
X-RAY DIFFRACTIONf_plane_restr0.004402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4603-1.48840.2741990.14011759X-RAY DIFFRACTION62
1.4884-1.51880.21951060.14371988X-RAY DIFFRACTION71
1.5188-1.55180.24891060.1422235X-RAY DIFFRACTION79
1.5518-1.58790.18821300.13212483X-RAY DIFFRACTION87
1.5879-1.62760.22741440.12372650X-RAY DIFFRACTION94
1.6276-1.67160.18191220.11892720X-RAY DIFFRACTION95
1.6716-1.72080.18451310.12072721X-RAY DIFFRACTION96
1.7208-1.77640.20261380.12642779X-RAY DIFFRACTION97
1.7764-1.83980.19291240.12842803X-RAY DIFFRACTION97
1.8398-1.91350.19261440.12622773X-RAY DIFFRACTION97
1.9135-2.00060.16871400.13182805X-RAY DIFFRACTION98
2.0006-2.10610.17311560.12962778X-RAY DIFFRACTION98
2.1061-2.2380.16041570.12832819X-RAY DIFFRACTION98
2.238-2.41080.1731320.13752837X-RAY DIFFRACTION98
2.4108-2.65330.18571400.14822878X-RAY DIFFRACTION99
2.6533-3.03710.16451650.14962869X-RAY DIFFRACTION99
3.0371-3.82580.17951590.14672924X-RAY DIFFRACTION99
3.8258-37.33510.15231670.163039X-RAY DIFFRACTION99

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