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- PDB-5hcl: Crystal Structure of the first bromodomain of BRD4 in complex with DMA -

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Basic information

Entry
Database: PDB / ID: 5hcl
TitleCrystal Structure of the first bromodomain of BRD4 in complex with DMA
ComponentsBromodomain-containing protein 4BRD4
KeywordsTranscription/transcription Inhibitor / Transcription-transcription 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 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
~{N},~{N}-dimethylethanamide / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsDong, J. / Weber, F.E. / Caflisch, A.
CitationJournal: Sci Rep / Year: 2017
Title: N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment.
Authors: Ghayor, C. / Gjoksi, B. / Dong, J. / Siegenthaler, B. / Caflisch, A. / Weber, F.E.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Jan 10, 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

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2493
Polymers15,0991
Non-polymers1492
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint1 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.615, 43.830, 78.459
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885
#2: Chemical ChemComp-5Y9 / ~{N},~{N}-dimethylethanamide / Dimethylacetamide


Mass: 87.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.14 Å3/Da / Density % sol: 42.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.20M Sodium Nitrate, 20% PEG 3350, 10% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000043 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000043 Å / Relative weight: 1
ReflectionResolution: 1.5→39.229 Å / Num. all: 21250 / Num. obs: 21250 / % possible obs: 99.2 % / Redundancy: 6.5 % / Rpim(I) all: 0.013 / Rrim(I) all: 0.034 / Rsym value: 0.031 / Net I/av σ(I): 12.944 / Net I/σ(I): 42.5 / Num. measured all: 137442
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.586.20.045141871930020.020.04528.298.1
1.58-1.686.60.04115.41931729120.0170.04132.799.7
1.68-1.796.60.03816.41806927380.0160.03836.199.7
1.79-1.946.40.036171606925180.0150.03640.399
1.94-2.126.80.03318.21610023780.0140.03347.499.7
2.12-2.376.60.03219.21410921430.0130.03250.399.5
2.37-2.746.20.0319.61161918790.0130.0350.998.4
2.74-3.356.70.0318.71087516300.0130.0356.199.3
3.35-4.746.30.02820.2811712900.0120.02857.599.6
4.74-39.2295.90.02819.444487600.0120.02853.898.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.23 Å39.23 Å
Translation5.23 Å39.23 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PCI

4pci


Resolution: 1.5→39.229 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 14.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1754 1051 4.96 %
Rwork0.1452 20151 -
obs0.1466 21202 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 49.73 Å2 / Biso mean: 12.5158 Å2 / Biso min: 4.03 Å2
Refinement stepCycle: final / Resolution: 1.5→39.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 10 260 1331
Biso mean--11.04 22.75 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061118
X-RAY DIFFRACTIONf_angle_d0.8191521
X-RAY DIFFRACTIONf_chiral_restr0.071160
X-RAY DIFFRACTIONf_plane_restr0.006199
X-RAY DIFFRACTIONf_dihedral_angle_d16.168433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4998-1.56810.17021220.13362456257897
1.5681-1.65070.17741290.129924852614100
1.6507-1.75420.17561340.1424922626100
1.7542-1.88960.17581450.14572460260599
1.8896-2.07980.17061350.146125192654100
2.0798-2.38070.22011480.14482507265599
2.3807-2.99920.15411100.15892545265598
2.9992-39.24290.16321280.14362687281599

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