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- PDB-5oww: Crystal structure of human BRD4(1) bromodomain in complex with UT22B -

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Basic information

Entry
Database: PDB / ID: 5oww
TitleCrystal structure of human BRD4(1) bromodomain in complex with UT22B
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-B0Q / 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 4, 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
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7278
Polymers60,3984
Non-polymers1,3294
Water15,205844
1
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4322
Polymers15,0991
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4322
Polymers15,0991
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4322
Polymers15,0991
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4322
Polymers15,0991
Non-polymers3321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.877, 41.924, 109.416
Angle α, β, γ (deg.)90.00, 92.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 4 / Fragment: Bromo domain 1, 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-B0Q / ~{N}-(3-methylbenzotriazol-5-yl)-1-(phenylmethyl)imidazole-2-carboxamide


Mass: 332.359 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H16N6O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999989 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 1.5→41.92 Å / Num. obs: 85408 / % possible obs: 97.9 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.459 / Num. unique obs: 4173 / CC1/2: 0.665 / % possible all: 98.4

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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→41.094 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2027 2000 2.34 %
Rwork0.1838 --
obs0.1842 85369 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4227 0 100 844 5171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094548
X-RAY DIFFRACTIONf_angle_d0.8976206
X-RAY DIFFRACTIONf_dihedral_angle_d12.8872790
X-RAY DIFFRACTIONf_chiral_restr0.046648
X-RAY DIFFRACTIONf_plane_restr0.006802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.31161440.30095920X-RAY DIFFRACTION98
1.5375-1.57910.3061350.26545907X-RAY DIFFRACTION98
1.5791-1.62560.251440.2415951X-RAY DIFFRACTION98
1.6256-1.6780.22221460.21345937X-RAY DIFFRACTION98
1.678-1.7380.23251380.20075948X-RAY DIFFRACTION98
1.738-1.80760.23811450.20335874X-RAY DIFFRACTION97
1.8076-1.88990.22821410.20685978X-RAY DIFFRACTION98
1.8899-1.98950.19631400.19736077X-RAY DIFFRACTION100
1.9895-2.11410.20971490.1886018X-RAY DIFFRACTION99
2.1141-2.27740.21941480.18255958X-RAY DIFFRACTION98
2.2774-2.50650.22841440.18395929X-RAY DIFFRACTION97
2.5065-2.86910.18881410.18095895X-RAY DIFFRACTION96
2.8691-3.61450.17341380.1665962X-RAY DIFFRACTION97
3.6145-41.10950.17311470.1566015X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -28.3469 Å / Origin y: -6.974 Å / Origin z: 27.4421 Å
111213212223313233
T0.0987 Å2-0.0029 Å20.0012 Å2-0.0684 Å20.0015 Å2--0.0857 Å2
L0.2854 °2-0.0136 °20.0097 °2-0.062 °20.0599 °2--0.1886 °2
S0.0192 Å °0.0232 Å °0.0153 Å °0.0016 Å °-0.0134 Å °-0.0001 Å °-0.0203 Å °-0.0039 Å °-0.0006 Å °
Refinement TLS groupSelection details: all

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