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- PDB-7zg1: BRD4 in complex with PepLite-Tyr -

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Basic information

Entry
Database: PDB / ID: 7zg1
TitleBRD4 in complex with PepLite-Tyr
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-T9J / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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)15,7263
Polymers15,2951
Non-polymers4312
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area7770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.620, 43.171, 79.418
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-T9J / Nalpha-acetyl-N-(3-bromoprop-2-yn-1-yl)-L-tyrosinamide


Mass: 339.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15BrN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
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: 0.911635 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911635 Å / Relative weight: 1
ReflectionResolution: 1.16→39.71 Å / Num. obs: 45643 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
6.35-39.7110.60.0343430.9980.0140.037
1.16-1.1812.85.68522180.3982.3846.172

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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: 1.16→39.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.839 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2502 2248 4.933 %
Rwork0.229 43323 -
all0.23 --
obs-45571 99.947 %
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: 24.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.454 Å20 Å2-0 Å2
2---1.961 Å20 Å2
3----0.494 Å2
Refinement stepCycle: LAST / Resolution: 1.16→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1076 0 26 147 1249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121137
X-RAY DIFFRACTIONr_angle_refined_deg1.831.6581545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.74724.560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3315199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.32153
X-RAY DIFFRACTIONr_chiral_restr0.1170.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02879
X-RAY DIFFRACTIONr_nbd_refined0.2410.2614
X-RAY DIFFRACTIONr_nbtor_refined0.3270.2784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2104
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.20.223
X-RAY DIFFRACTIONr_mcbond_it1.8481.992517
X-RAY DIFFRACTIONr_mcangle_it2.5292.98645
X-RAY DIFFRACTIONr_scbond_it3.6732.399620
X-RAY DIFFRACTIONr_scangle_it4.8893.459899
X-RAY DIFFRACTIONr_lrange_it9.04830.7951896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.16-1.190.4451740.4643136X-RAY DIFFRACTION99.8793
1.19-1.2230.4591690.4353092X-RAY DIFFRACTION99.9693
1.223-1.2580.4011450.4012987X-RAY DIFFRACTION99.9362
1.258-1.2970.4051540.4182912X-RAY DIFFRACTION100
1.297-1.3390.3661510.3532826X-RAY DIFFRACTION100
1.339-1.3860.3611640.3322699X-RAY DIFFRACTION100
1.386-1.4390.3751330.3032668X-RAY DIFFRACTION100
1.439-1.4970.351280.2892545X-RAY DIFFRACTION100
1.497-1.5640.2631130.2552466X-RAY DIFFRACTION100
1.564-1.640.2561190.2212345X-RAY DIFFRACTION100
1.64-1.7290.2421090.2092243X-RAY DIFFRACTION100
1.729-1.8340.2751080.2082111X-RAY DIFFRACTION100
1.834-1.960.281280.2341992X-RAY DIFFRACTION99.9529
1.96-2.1170.257740.2141883X-RAY DIFFRACTION100
2.117-2.3190.236890.2111721X-RAY DIFFRACTION100
2.319-2.5930.262800.2051572X-RAY DIFFRACTION100
2.593-2.9930.211640.2081406X-RAY DIFFRACTION100
2.993-3.6650.211620.21213X-RAY DIFFRACTION100
3.665-5.1770.169450.156950X-RAY DIFFRACTION100
5.177-39.710.156390.198556X-RAY DIFFRACTION100

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