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- PDB-6zel: CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 6zel
TitleCRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5
ComponentsBromodomain-containing protein 4BRD4
KeywordsCELL CYCLE / BROMODOMAIN-CONTAINING PROTEIN 4 ISOFORM LONG / BRD4 / BROMODOMAIN-CONTAINING PROTEIN 4 / CAP / HUNK1 / MCAP / MITOTIC CHROMOSOME ASSOCIATED PROTEIN
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 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. ...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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-QGQ / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.12 Å
AuthorsKrojer, T. / Martinez-Cartro, M. / Picaud, S. / Filippakopoulos, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Barril, X. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5
Authors: Martinez-Cartro, M. / Barril, X.
History
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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)15,5215
Polymers15,0991
Non-polymers4224
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area490 Å2
ΔGint6 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.235, 44.141, 78.441
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 / BRD4 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-QGQ / 3,5-dimethyl-4-[(6-methylpyrimidin-4-yl)sulfanylmethyl]-1,2-oxazole


Mass: 235.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N3OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.15 Å3/Da / Density % sol: 42.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M bis-tris-propane pH 7.9, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.12→39.221 Å / Num. obs: 48062 / % possible obs: 95.4 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 25.6
Reflection shellResolution: 1.12→1.14 Å / Num. unique obs: 1773 / CC1/2: 0.994

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3MXF

3mxf


Resolution: 1.12→39.221 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.579 / SU ML: 0.013 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1466 2406 5.012 %
Rwork0.1249 45602 -
all0.126 --
obs-48008 95.003 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 11.188 Å2
Baniso -1Baniso -2Baniso -3
1--0.145 Å20 Å2-0 Å2
2---0.429 Å20 Å2
3---0.574 Å2
Refinement stepCycle: LAST / Resolution: 1.12→39.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1053 0 28 189 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131146
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171059
X-RAY DIFFRACTIONr_angle_refined_deg1.7261.6681560
X-RAY DIFFRACTIONr_angle_other_deg1.5691.5882483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0635133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85225.08857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.13115203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.104153
X-RAY DIFFRACTIONr_chiral_restr0.1050.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02211
X-RAY DIFFRACTIONr_nbd_refined0.2330.2261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.2943
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2558
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.284
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.23
X-RAY DIFFRACTIONr_nbd_other0.1980.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1080.220
X-RAY DIFFRACTIONr_mcbond_it10.2290.821524
X-RAY DIFFRACTIONr_mcbond_other10.2190.822525
X-RAY DIFFRACTIONr_mcangle_it9.1361.225659
X-RAY DIFFRACTIONr_mcangle_other9.1291.231660
X-RAY DIFFRACTIONr_scbond_it1.5681.066622
X-RAY DIFFRACTIONr_scbond_other1.5671.067623
X-RAY DIFFRACTIONr_scangle_it7.9591.521901
X-RAY DIFFRACTIONr_scangle_other7.9551.522902
X-RAY DIFFRACTIONr_lrange_it9.49510.9831365
X-RAY DIFFRACTIONr_lrange_other9.50210.9941363
X-RAY DIFFRACTIONr_rigid_bond_restr2.19532205
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
1.12-1.1490.1371310.09526560.09736740.9770.98475.85740.087
1.149-1.1810.1131690.08831390.08935920.9860.98992.09350.081
1.181-1.2150.1071690.08831270.08934880.9870.98994.49540.085
1.215-1.2520.1221770.0930560.09234040.9830.98794.97650.086
1.252-1.2930.1191570.08729780.08932900.9830.98995.28880.085
1.293-1.3380.1241420.08929230.0932110.9810.98795.45310.087
1.338-1.3890.1261390.09228250.09330790.9830.98796.2650.091
1.389-1.4460.121730.09126870.09329600.9830.98896.62160.093
1.446-1.510.1191330.09226270.09328540.9840.98796.70640.094
1.51-1.5830.121120.09625380.09727390.9840.98796.75060.101
1.583-1.6690.1331380.10124170.10326150.9810.98497.70550.108
1.669-1.770.1441090.11623160.11724910.9750.98197.35050.128
1.77-1.8920.1371190.11921380.1222910.9780.98298.51590.135
1.892-2.0430.1431020.12620440.12721890.9780.97998.03560.145
2.043-2.2370.151800.1319050.1320130.9750.97998.6090.154
2.237-2.50.1531110.14417040.14418400.9730.97598.64130.175
2.5-2.8850.18690.15815540.15916320.960.96999.44850.197
2.885-3.5290.161810.1612950.1613870.9730.97499.20690.205
3.529-4.970.128570.1510460.14911140.9820.9899.01260.197
4.97-39.2210.293380.2216270.2266700.9730.96699.25370.299

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