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- PDB-5e0r: Crystal Structure of the first bromodomain of BRD4 in complex with AYC -

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Basic information

Entry
Database: PDB / ID: 5e0r
TitleCrystal Structure of the first bromodomain of BRD4 in complex with AYC
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 T-helper 17 cell lineage commitment / 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 ...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 T-helper 17 cell lineage commitment / 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-5J5 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.352 Å
AuthorsDong, J. / Caflisch, A.
CitationJournal: To Be Published
Title: Crystal Structure of the first bromodomain of BRD4 in complex with AYC
Authors: Dong, J. / Caflish, A.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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)17,3477
Polymers15,0991
Non-polymers2,2476
Water2,630146
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint3 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.776, 44.538, 77.964
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
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-5J5 / 2-[(chloroacetyl)amino]-5-[(E)-(4-sulfophenyl)diazenyl]benzenesulfonic acid


Mass: 433.844 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H12ClN3O7S2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
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 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.352→38.982 Å / Num. all: 27342 / Num. obs: 27342 / % possible obs: 95.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 12.24 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.056 / Rsym value: 0.051 / Net I/av σ(I): 8.54 / Net I/σ(I): 15.7 / Num. measured all: 141751
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
1.352-1.432.10.3112617429900.2350.3112.673.1
1.43-1.514.10.2352.91558037890.130.2355.297.4
1.51-1.625.90.1574.42151036560.0710.1578.599.7
1.62-1.755.80.1235.51974434200.0560.12311.299.3
1.75-1.916.10.0828.51944531670.0360.08215.599.8
1.91-2.145.70.06110.91645328740.0280.06120.899.4
2.14-2.4760.05212.61518725360.0230.05226.199.3
2.47-3.025.70.04613.31251421810.0210.04629.299.4
3.02-4.285.60.03915.7951917050.0180.03934.699
4.28-44.5385.50.03417.6562510240.0150.03434.899.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.35 Å38.98 Å
Translation1.35 Å38.98 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
PHENIX1.10-2155refinement
PDB_EXTRACT3.15data extraction
XDSVERSION Jun 17, 2015 BUILT=20150617data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PCI

4pci


Resolution: 1.352→38.982 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 1342 4.93 %
Rwork0.1709 25878 -
obs0.1722 27220 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.54 Å2 / Biso mean: 18.0729 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 1.352→38.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 139 146 1346
Biso mean--28.21 29.49 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091269
X-RAY DIFFRACTIONf_angle_d1.3151745
X-RAY DIFFRACTIONf_chiral_restr0.051173
X-RAY DIFFRACTIONf_plane_restr0.007221
X-RAY DIFFRACTIONf_dihedral_angle_d17.317475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3524-1.40080.3025780.2781767184566
1.4008-1.45690.24271050.21042429253490
1.4569-1.52320.21871350.1822652278798
1.5232-1.60350.17731370.16472687282499
1.6035-1.70390.19471490.17022648279799
1.7039-1.83550.22131660.16632672283899
1.8355-2.02020.18261450.16112693283899
2.0202-2.31250.1911400.15412723286399
2.3125-2.91340.19451430.17622727287099
2.9134-38.99820.19291440.16742880302499
Refinement TLS params.Method: refined / Origin x: 11.8169 Å / Origin y: -3.0253 Å / Origin z: -8.1222 Å
111213212223313233
T0.0615 Å20.003 Å20.0044 Å2-0.0776 Å20.0057 Å2--0.0806 Å2
L0.4506 °20.0073 °2-0.1387 °2-0.651 °2-0.0537 °2--0.831 °2
S-0.0168 Å °-0.015 Å °-0.0108 Å °0.0184 Å °0.0042 Å °0.015 Å °0.0589 Å °0.0175 Å °-0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA42 - 168
2X-RAY DIFFRACTION1allB1 - 5
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 148

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