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- PDB-7zfu: BRD4 in complex with PepLite-Pro -

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Basic information

Entry
Database: PDB / ID: 7zfu
TitleBRD4 in complex with PepLite-Pro
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / FragLites / anomalous / BRD4 / Fragment screening
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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-IS6 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsTurberville, S. / Martin, M.P. / Hope, I. / Noble, M.E.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Cancer Research UKC57659/A27310 United Kingdom
Cancer Research UKC1362/A20263 United Kingdom
Cancer Research UKC2215/A21421 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions.
Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / ...Authors: Davison, G. / Martin, M.P. / Turberville, S. / Dormen, S. / Heath, R. / Heptinstall, A.B. / Lawson, M. / Miller, D.C. / Ng, Y.M. / Sanderson, J.N. / Hope, I. / Wood, D.J. / Cano, C. / Endicott, J.A. / Hardcastle, I.R. / Noble, M.E.M. / Waring, M.J.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8445
Polymers15,2951
Non-polymers5494
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-1 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.868, 43.397, 80.407
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: 15294.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-IS6 / (2R)-N-(3-bromanylprop-2-ynyl)-1-ethanoyl-pyrrolidine-2-carboxamide


Mass: 273.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13BrN2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Buffer system 3 (1 M Tris, 1 M BICINE, pH 8.5), 34-44% Precipitant Solution 3 (20% PEG 4000, 40%) and 60-80 mM Halogens Mix (NaF, NaBr and NaI) solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.29→38.19 Å / Num. obs: 33926 / % possible obs: 99.3 % / Redundancy: 7.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.056 / Rrim(I) all: 0.112 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.07-38.195.90.1112630.8560.0660.13
1.29-1.315.52.1615920.3051.4662.626

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LRQ

5lrq


Resolution: 1.29→38.19 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.992 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2041 1606 4.742 %
Rwork0.1903 32265 -
all0.191 --
obs-33871 99.209 %
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: 20.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.392 Å20 Å2-0 Å2
2---0.456 Å20 Å2
3---0.064 Å2
Refinement stepCycle: LAST / Resolution: 1.29→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 33 107 1216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0121151
X-RAY DIFFRACTIONr_angle_refined_deg2.2331.6571563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05224.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63115201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.716153
X-RAY DIFFRACTIONr_chiral_restr0.1260.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02883
X-RAY DIFFRACTIONr_nbd_refined0.2410.2537
X-RAY DIFFRACTIONr_nbtor_refined0.3280.2797
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.273
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3950.218
X-RAY DIFFRACTIONr_mcbond_it1.7181.585522
X-RAY DIFFRACTIONr_mcangle_it2.5312.367653
X-RAY DIFFRACTIONr_scbond_it3.8312.057629
X-RAY DIFFRACTIONr_scangle_it5.4572.915909
X-RAY DIFFRACTIONr_lrange_it7.80924.2791798
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.3230.359990.3262256X-RAY DIFFRACTION94.7305
1.323-1.360.3071070.292232X-RAY DIFFRACTION96.7729
1.36-1.3990.315990.2532250X-RAY DIFFRACTION99.2815
1.399-1.4420.2211020.2532166X-RAY DIFFRACTION99.7361
1.442-1.4890.2581140.2192106X-RAY DIFFRACTION99.5516
1.489-1.5420.1981270.2042018X-RAY DIFFRACTION99.6747
1.542-1.60.227980.1871990X-RAY DIFFRACTION99.7135
1.6-1.6650.216940.181898X-RAY DIFFRACTION99.8496
1.665-1.7390.179940.1681854X-RAY DIFFRACTION99.8974
1.739-1.8240.1941010.1741731X-RAY DIFFRACTION100
1.824-1.9230.186740.1741682X-RAY DIFFRACTION100
1.923-2.0390.215850.1761581X-RAY DIFFRACTION99.94
2.039-2.180.207720.1881504X-RAY DIFFRACTION99.9366
2.18-2.3540.183620.1831412X-RAY DIFFRACTION100
2.354-2.5790.247700.1811286X-RAY DIFFRACTION100
2.579-2.8830.197570.1731201X-RAY DIFFRACTION100
2.883-3.3280.188600.1741040X-RAY DIFFRACTION100
3.328-4.0750.143390.152908X-RAY DIFFRACTION100
4.075-5.7550.164300.196722X-RAY DIFFRACTION100
5.755-38.190.282220.272429X-RAY DIFFRACTION99.5585

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