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- PDB-7ugf: First bromodomain of BRD4 liganded with BMS-536924 -

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Basic information

Entry
Database: PDB / ID: 7ugf
TitleFirst bromodomain of BRD4 liganded with BMS-536924
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / bromodomain / small molecule ligand / complex
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-like ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-N6I / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSchonbrunn, E. / Bikowitz, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of CBP and EP300 interaction with kinase inhibitors
Authors: Schonbrunn, E. / Bikowitz, M.
History
DepositionMar 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)15,8907
Polymers15,0991
Non-polymers7906
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.400, 44.260, 78.640
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 / 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 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-N6I / (3M)-4-{[(2S)-2-(3-chlorophenyl)-2-hydroxyethyl]amino}-3-[4-methyl-6-(morpholin-4-yl)-1H-benzimidazol-2-yl]pyridin-2(1H)-one


Mass: 479.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 42.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.45→39.32 Å / Num. obs: 23514 / % possible obs: 98.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 19.7
Reflection shellResolution: 1.45→1.49 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1512 / CC1/2: 0.952 / Rrim(I) all: 0.247

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KJ0

5kj0


Resolution: 1.45→39.32 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 1529 6.5 %
Rwork0.1712 21983 -
obs0.1725 23512 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.52 Å2 / Biso mean: 19.414 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.45→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 54 152 1264
Biso mean--29.48 28.18 -
Num. residues----127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.50.23881220.20671752187488
1.5-1.550.25911350.18961935207097
1.55-1.610.2271380.178919872125100
1.61-1.690.21731380.176419832121100
1.69-1.770.22491410.180820332174100
1.77-1.890.21641380.18619832121100
1.89-2.030.18461390.176320052144100
2.03-2.240.171420.165520422184100
2.24-2.560.15851410.181920252166100
2.56-3.220.19351440.171220702214100
3.23-39.320.18111510.155921682319100
Refinement TLS params.Method: refined / Origin x: 12.0952 Å / Origin y: 3.2729 Å / Origin z: 8.4863 Å
111213212223313233
T0.0542 Å2-0.0046 Å2-0.0058 Å2-0.0954 Å20.0078 Å2--0.0947 Å2
L0.7783 °2-0.1497 °20.1869 °2-1.8078 °20.1482 °2--1.7062 °2
S-0.0137 Å °-0.0082 Å °0.016 Å °0.043 Å °0.024 Å °-0.0024 Å °-0.0256 Å °-0.0207 Å °-0.007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA42 - 168
2X-RAY DIFFRACTION1allI1
3X-RAY DIFFRACTION1allE401 - 901
4X-RAY DIFFRACTION1allQ1 - 153

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