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- PDB-5owm: Crystal structure of human BRD4(1) bromodomain in complex with UT48 -

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Basic information

Entry
Database: PDB / ID: 5owm
TitleCrystal structure of human BRD4(1) bromodomain in complex with UT48
ComponentsBromodomain-containing protein 4BRD4
KeywordsDNA BINDING PROTEIN / BRD4 bromodomain 1(BRP4(1)) / Inhibitor
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 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 ...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 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 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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-B0N / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsZhu, J. / Caflisch, A.
CitationJournal: Acs Cent.Sci. / Year: 2018
Title: Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple).
Authors: Batiste, L. / Unzue, A. / Dolbois, A. / Hassler, F. / Wang, X. / Deerain, N. / Zhu, J. / Spiliotopoulos, D. / Nevado, C. / Caflisch, A.
History
DepositionSep 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3532
Polymers15,0991
Non-polymers2531
Water3,243180
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.452, 47.094, 78.731
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 / BRD4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1
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-B0N / [3-[(3-methylbenzotriazol-5-yl)methyl]phenyl]methanol


Mass: 253.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 1.99 Å3/Da / Density % sol: 38.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: HEPES, Sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.5→47.09 Å / Num. obs: 19968 / % possible obs: 99.7 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 18.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.636 / Num. unique obs: 965 / CC1/2: 0.967 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.5→40.415 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.14
RfactorNum. reflection% reflection
Rfree0.1972 1992 10.01 %
Rwork0.1685 --
obs0.1714 19901 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→40.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1031 0 19 180 1230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051090
X-RAY DIFFRACTIONf_angle_d0.8051489
X-RAY DIFFRACTIONf_dihedral_angle_d1.937940
X-RAY DIFFRACTIONf_chiral_restr0.044159
X-RAY DIFFRACTIONf_plane_restr0.005211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.26321390.24121253X-RAY DIFFRACTION99
1.5375-1.57910.27891390.2151241X-RAY DIFFRACTION99
1.5791-1.62560.24741410.19481274X-RAY DIFFRACTION100
1.6256-1.6780.23431400.18391252X-RAY DIFFRACTION100
1.678-1.7380.23881410.17761269X-RAY DIFFRACTION99
1.738-1.80760.19991400.1571262X-RAY DIFFRACTION99
1.8076-1.88990.20761390.17131250X-RAY DIFFRACTION100
1.8899-1.98950.19531410.16641266X-RAY DIFFRACTION99
1.9895-2.11420.18751410.15941270X-RAY DIFFRACTION99
2.1142-2.27740.20261420.15491271X-RAY DIFFRACTION100
2.2774-2.50650.20841440.18041300X-RAY DIFFRACTION100
2.5065-2.86910.21531440.18651295X-RAY DIFFRACTION100
2.8691-3.61450.18281470.16381325X-RAY DIFFRACTION100
3.6145-40.43010.17171540.15431381X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.7084 Å / Origin y: 43.7449 Å / Origin z: 8.3759 Å
111213212223313233
T0.1624 Å2-0.0004 Å20.0199 Å2-0.1071 Å2-0.0015 Å2--0.1098 Å2
L0.5125 °20.1607 °2-0.2516 °2-0.2529 °20.1612 °2--0.4232 °2
S0.0377 Å °-0.015 Å °0.0154 Å °-0.0126 Å °0.0116 Å °-0.0429 Å °-0.107 Å °0.0447 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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