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- PDB-4whw: Direct photocapture of bromodomains using tropolone chemical probes -

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Basic information

Entry
Database: PDB / ID: 4whw
TitleDirect photocapture of bromodomains using tropolone chemical probes
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / BROMO domain / BRD4 / inhibitor / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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-like ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3OT / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.345 Å
AuthorsHett, E.C. / Piatnitski Chekler, E.L. / Basak, A. / Bonin, P.D. / Denny, R.A. / Flick, A.C. / Geoghegan, K.F. / Liu, S. / Pletcher, M.T. / Robinson, R.P. ...Hett, E.C. / Piatnitski Chekler, E.L. / Basak, A. / Bonin, P.D. / Denny, R.A. / Flick, A.C. / Geoghegan, K.F. / Liu, S. / Pletcher, M.T. / Robinson, R.P. / Sahasrabudhe, P. / Salter, S. / Stock, I.A. / Jones, L.H.
CitationJournal: To Be Published
Title: Direct photocapture of bromodomains using tropolone chemical probes
Authors: Hett, E.C. / Piatnitski Chekler, E.L. / Basak, A. / Bonin, P.D. / Denny, R.A. / Flick, A.C. / Geoghegan, K.F. / Liu, S. / Pletcher, M.T. / Robinson, R.P. / Sahasrabudhe, P. / Salter, S. / ...Authors: Hett, E.C. / Piatnitski Chekler, E.L. / Basak, A. / Bonin, P.D. / Denny, R.A. / Flick, A.C. / Geoghegan, K.F. / Liu, S. / Pletcher, M.T. / Robinson, R.P. / Sahasrabudhe, P. / Salter, S. / Stock, I.A. / Jones, L.H.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6313
Polymers15,0991
Non-polymers5322
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.830, 50.591, 57.468
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: 15099.380 Da / Num. of mol.: 1 / Fragment: UNP residues 44-168
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-3OT / 2-methoxy-4-{1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazol-5-yl}cyclohepta-2,4,6-trien-1-one


Mass: 469.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H31N3O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Screen using Hampton Research HT and Index kits

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.345→57.468 Å / Num. all: 153114 / Num. obs: 26339 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 15.29 Å2 / Net I/σ(I): 19.1
Reflection shellResolution: 1.345→1.349 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 2.3 / % possible all: 77.5

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.345→15.88 Å / Cor.coef. Fo:Fc: 0.9591 / Cor.coef. Fo:Fc free: 0.9474 / SU R Cruickshank DPI: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.06 / SU Rfree Blow DPI: 0.06 / SU Rfree Cruickshank DPI: 0.058
RfactorNum. reflection% reflectionSelection details
Rfree0.2009 1330 5.06 %RANDOM
Rwork0.1799 ---
obs0.181 26262 98.29 %-
Displacement parametersBiso mean: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.6095 Å20 Å20 Å2
2---0.7387 Å20 Å2
3---0.1292 Å2
Refine analyzeLuzzati coordinate error obs: 0.145 Å
Refinement stepCycle: 1 / Resolution: 1.345→15.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1033 0 39 125 1197
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011142HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.981584HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d393SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes32HARMONIC2
X-RAY DIFFRACTIONt_gen_planes186HARMONIC5
X-RAY DIFFRACTIONt_it1142HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion15.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion137SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1412SEMIHARMONIC4
LS refinement shellResolution: 1.34→1.4 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2397 125 4.93 %
Rwork0.2023 2408 -
all0.2042 2533 -
obs--98.29 %
Refinement TLS params.Method: refined / Origin x: -6.4932 Å / Origin y: 9.3878 Å / Origin z: -16.4799 Å
111213212223313233
T-0.1182 Å20 Å2-0.0001 Å2--0.107 Å20.0167 Å2---0.1193 Å2
L0.764 °2-0.1544 °2-0.3891 °2-0.8042 °20.235 °2--0.8557 °2
S-0.0451 Å °-0.0724 Å °-0.0458 Å °0.0134 Å °-0.0064 Å °-0.022 Å °-0.0055 Å °0.0472 Å °0.0516 Å °
Refinement TLS groupSelection details: { A|* }

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