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

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Basic information

Entry
Database: PDB / ID: 8qap
TitleCrystal Structure of the first bromodomain of BRD4 in complex with acetyl-pyrrole derivative compound 2
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 / 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 / condensed nuclear chromosome / histone reader activity / : ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / 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 / condensed nuclear chromosome / histone reader activity / : / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
: / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)15,5414
Polymers15,0991
Non-polymers4423
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint5 kcal/mol
Surface area7530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.101, 44.369, 78.005
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: The 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-Q9U / 2-[4-(3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-2~{H}-isoindol-1-yl)-1,3-thiazol-2-yl]guanidine


Mass: 317.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19N5OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 42.15 %
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: 1.4→44.37 Å / Num. obs: 26131 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.033 / Rrim(I) all: 0.114 / Χ2: 0.95 / Net I/σ(I): 12.5 / Num. measured all: 318947
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 100 % / Redundancy: 12.6 % / Rmerge(I) obs: 1.449 / Num. measured all: 16195 / Num. unique obs: 1286 / CC1/2: 0.767 / Rpim(I) all: 0.422 / Rrim(I) all: 1.511 / Χ2: 0.88 / Net I/σ(I) obs: 2.1

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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: 1.4→39.002 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 1265 4.85 %
Rwork0.1508 --
obs0.1526 26062 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→39.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 30 133 1215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081125
X-RAY DIFFRACTIONf_angle_d0.9421534
X-RAY DIFFRACTIONf_dihedral_angle_d19.681437
X-RAY DIFFRACTIONf_chiral_restr0.068159
X-RAY DIFFRACTIONf_plane_restr0.006198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.45610.24661430.2032704X-RAY DIFFRACTION100
1.4561-1.52240.20041480.16872704X-RAY DIFFRACTION100
1.5224-1.60260.18261290.14572730X-RAY DIFFRACTION100
1.6026-1.70310.19521300.13912722X-RAY DIFFRACTION100
1.7031-1.83450.19691280.14082726X-RAY DIFFRACTION100
1.8345-2.01920.17721430.12972744X-RAY DIFFRACTION100
2.0192-2.31130.16781590.12492749X-RAY DIFFRACTION100
2.3113-2.91190.16871380.14882791X-RAY DIFFRACTION100
2.9119-39.0020.19431470.16452927X-RAY DIFFRACTION100

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