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- PDB-5uep: BRD4_BD2_A-581577 -

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Basic information

Entry
Database: PDB / ID: 5uep
TitleBRD4_BD2_A-581577
ComponentsBromodomain-containing protein 4
KeywordsSIGNALING PROTEIN/INHIBITOR / SIGNALING PROTEIN-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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 I / Brdt, bromodomain, repeat II / 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 I / Brdt, bromodomain, repeat II / 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-88P / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsPark, C.H.
CitationJournal: To Be Published
Title: Complex structure of BRD4_BD2_A-581577
Authors: Park, C.H.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)13,0282
Polymers12,8071
Non-polymers2211
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.802, 73.604, 33.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

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Components

#1: Protein Bromodomain-containing protein 4 / Protein HUNK1


Mass: 12806.933 Da / Num. of mol.: 1 / Fragment: residues 352-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: O60885
#2: Chemical ChemComp-88P / ethyl 3-methyl-4-oxo-4,5,6,7-tetrahydro-2H-isoindole-1-carboxylate


Mass: 221.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: Protein Buffer : 10 mM HEPES PH 7.5 100 mM NaCl 5 mM DTT Crystallization : 15 % (v/v) Ethanol Tris 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→73.6 Å / Num. obs: 14367 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 30.39 Å2 / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
XDS2.11.7data reduction
SCALAdata scaling
Cootmodel building
BUSTER2.11.7refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo BRD4_BD2

Resolution: 1.77→36.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / Rfactor Rfree error: 0.02 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.113 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.219 711 4.98 %RANDOM
Rwork0.182 ---
obs0.184 14278 99.9 %-
Displacement parametersBiso mean: 34.69 Å2
Baniso -1Baniso -2Baniso -3
1--5.9417 Å20 Å20 Å2
2--6.4316 Å20 Å2
3----0.4899 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.77→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms891 0 16 139 1046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01938HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.91257HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d337SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes21HARMONIC2
X-RAY DIFFRACTIONt_gen_planes136HARMONIC5
X-RAY DIFFRACTIONt_it938HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion15.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion111SEMIHARMONIC5
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_contact1214SEMIHARMONIC4
LS refinement shellResolution: 1.77→1.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.257 162 5.63 %
Rwork0.211 2716 -
all0.214 2878 -
obs--99.97 %

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