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- PDB-4bjx: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH GSK1324726A (I-BET726) -

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Basic information

Entry
Database: PDB / ID: 4bjx
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH GSK1324726A (I-BET726)
ComponentsBROMODOMAIN-CONTAINING PROTEIN 4
KeywordsDNA BINDING PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER
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-73B / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsChung, C.
CitationJournal: Plos One / Year: 2013
Title: Bet Inhibition Silences Expression of Mycn and Bcl2 and Induces Cytotoxicity in Neuroblastoma Tumor Models.
Authors: Wyce, A. / Ganji, G. / Smitheman, K.N. / Chung, C. / Korenchuk, S. / Bai, Y. / Barbash, O. / Le, B. / Craggs, P.D. / Mccabe, M.T. / Kennedy-Wilson, K.M. / Sanchez, L.V. / Gosmini, R.L. / ...Authors: Wyce, A. / Ganji, G. / Smitheman, K.N. / Chung, C. / Korenchuk, S. / Bai, Y. / Barbash, O. / Le, B. / Craggs, P.D. / Mccabe, M.T. / Kennedy-Wilson, K.M. / Sanchez, L.V. / Gosmini, R.L. / Parr, N. / Mchugh, C.F. / Dhanak, D. / Prinjha, R.K. / Auger, K.R. / Tummino, P.J.
History
DepositionApr 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references / Source and taxonomy
Revision 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)18,3742
Polymers17,9391
Non-polymers4351
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.780, 47.906, 58.757
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 / BRD4


Mass: 17939.486 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-73B / 4-[(2S,4R)-1-acetyl-4-[(4-chlorophenyl)amino]-2-methyl-1,2,3,4-tetrahydroquinolin-6-yl]benzoic acid


Mass: 434.915 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23ClN2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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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: 1.59 Å3/Da / Density % sol: 22.07 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.5
Details: 20% PEG3350, 0.2M NAK,TARTRATE, 0.1M BISTRISPROPANE PH 6.5, 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.59→58.76 Å / Num. obs: 17351 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 55.3
Reflection shellResolution: 1.59→1.68 Å / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 21.1 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→25.04 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.381 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18518 879 5.1 %RANDOM
Rwork0.15663 ---
obs0.15803 16423 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.781 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.59→25.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 31 297 1389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191155
X-RAY DIFFRACTIONr_bond_other_d0.0010.02799
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.9561577
X-RAY DIFFRACTIONr_angle_other_deg0.83231968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.815133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66925.92654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.315205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.726153
X-RAY DIFFRACTIONr_chiral_restr0.0640.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 49 -
Rwork0.178 947 -
obs--83.77 %

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