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- PDB-8qan: Crystal Structure of the first bromodomain of BRD4 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8qan
TitleCrystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 79
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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, conserved site ...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, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-GKI / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsDalle Vedove, A. / Cazzanelli, G. / Lolli, G.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG 2017 - ID. 19882 Italy
CitationJournal: Protein Sci. / Year: 2024
Title: Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors.
Authors: Cazzanelli, G. / Dalle Vedove, A. / Sbardellati, N. / Valer, L. / Caflisch, A. / Lolli, G.
History
DepositionAug 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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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)15,5223
Polymers15,0991
Non-polymers4232
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.062, 44.476, 78.105
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 / Mutation: First bromodomain (residues 1796-1899)
Source method: isolated from a genetically manipulated source
Details: First two residues SM derive from the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O60885
#2: Chemical ChemComp-GKI / 1-[2-methyl-4-(3-methylbutyl)-5-(2-piperazin-1-yl-1,3-thiazol-4-yl)-1~{H}-pyrrol-3-yl]ethanone


Mass: 360.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N4OS / Feature type: SUBJECT OF INVESTIGATION
#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.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 16% PEG 3350, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→39.053 Å / Num. obs: 35800 / % possible obs: 98.2 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.028 / Rrim(I) all: 0.098 / Χ2: 0.99 / Net I/σ(I): 14
Reflection shellResolution: 1.25→1.27 Å / % possible obs: 95.2 % / Redundancy: 12.4 % / Rmerge(I) obs: 1.215 / Num. measured all: 21120 / Num. unique obs: 1710 / CC1/2: 0.793 / Rpim(I) all: 0.355 / Rrim(I) all: 1.267 / Χ2: 1.04 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→39.053 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1757 1797 5.03 %
Rwork0.1544 --
obs0.1555 35740 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→39.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 29 135 1216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091139
X-RAY DIFFRACTIONf_angle_d1.1181556
X-RAY DIFFRACTIONf_dihedral_angle_d17.733452
X-RAY DIFFRACTIONf_chiral_restr0.074162
X-RAY DIFFRACTIONf_plane_restr0.007201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.28380.24411350.22252524X-RAY DIFFRACTION96
1.2838-1.32160.21811400.18872519X-RAY DIFFRACTION96
1.3216-1.36430.20471380.17462527X-RAY DIFFRACTION97
1.3643-1.4130.2041540.15462533X-RAY DIFFRACTION97
1.413-1.46960.17241310.14042569X-RAY DIFFRACTION97
1.4696-1.53650.18011270.13022589X-RAY DIFFRACTION97
1.5365-1.61750.1671240.12512615X-RAY DIFFRACTION99
1.6175-1.71880.15861460.12892581X-RAY DIFFRACTION98
1.7188-1.85160.17411250.13812647X-RAY DIFFRACTION99
1.8516-2.03790.15331460.13752629X-RAY DIFFRACTION99
2.0379-2.33270.16161460.1352672X-RAY DIFFRACTION99
2.3327-2.93890.17571470.15672690X-RAY DIFFRACTION99
2.9389-39.0530.18091380.17422848X-RAY DIFFRACTION99

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