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- PDB-5o97: Crystal structure of human BRD4(1) bromodomain in complex with JR... -

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Basic information

Entry
Database: PDB / ID: 5o97
TitleCrystal structure of human BRD4(1) bromodomain in complex with JRMBR4106
ComponentsBromodomain-containing protein 4
KeywordsDNA BINDING PROTEIN / BRD4 bromodomain 1(BRP4(1)) / Inhibitor
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 / chromatin / 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-9OE / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhu, J. / Marchand, J.R. / Caflisch, A.
CitationJournal: To Be Published
Title: Crystal structure of human BRD4(1) bromodomain in complex with JRMBR4106
Authors: Zhu, J. / Marchand, J.R. / Caflisch, A.
History
DepositionJun 15, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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)15,4123
Polymers15,0991
Non-polymers3122
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.316, 44.511, 78.397
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
Source method: isolated from a genetically manipulated source
Details: EDO / Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-9OE / (5~{Z})-4-azanyl-5-[(3-methoxy-4-oxidanyl-phenyl)methylidene]-1,3-thiazol-2-one


Mass: 250.274 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10N2O3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES, pH8.0, 30% PEG5000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.3→44.51 Å / Num. obs: 32824 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 1605 / CC1/2: 0.905 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.3→39.199 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.69
RfactorNum. reflection% reflection
Rfree0.1993 1998 6.1 %
Rwork0.1786 --
obs0.1799 32763 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→39.199 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1057 0 21 240 1318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061135
X-RAY DIFFRACTIONf_angle_d1.0261548
X-RAY DIFFRACTIONf_dihedral_angle_d9.932717
X-RAY DIFFRACTIONf_chiral_restr0.075162
X-RAY DIFFRACTIONf_plane_restr0.006201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.33250.26451390.25452162X-RAY DIFFRACTION99
1.3325-1.36860.26721410.25272148X-RAY DIFFRACTION100
1.3686-1.40880.23761400.22392166X-RAY DIFFRACTION100
1.4088-1.45430.21481420.20322178X-RAY DIFFRACTION99
1.4543-1.50630.20441400.18442158X-RAY DIFFRACTION100
1.5063-1.56660.17691410.17592162X-RAY DIFFRACTION100
1.5666-1.63790.19341420.16912196X-RAY DIFFRACTION100
1.6379-1.72430.20161420.1662178X-RAY DIFFRACTION100
1.7243-1.83230.21241420.17892188X-RAY DIFFRACTION100
1.8323-1.97380.20141420.17812206X-RAY DIFFRACTION100
1.9738-2.17240.20411430.17112204X-RAY DIFFRACTION99
2.1724-2.48670.21591450.18072219X-RAY DIFFRACTION100
2.4867-3.13270.20251460.17972249X-RAY DIFFRACTION100
3.1327-39.21630.17891530.16722351X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 25.4529 Å / Origin y: 40.9663 Å / Origin z: 8.7999 Å
111213212223313233
T0.1 Å20.0002 Å20.0108 Å2-0.1161 Å2-0.0055 Å2--0.1179 Å2
L0.4935 °20.1738 °2-0.1128 °2-1.0244 °2-0.0131 °2--1.1098 °2
S-0.0052 Å °-0.0142 Å °-0.0312 Å °0.0347 Å °0.0014 Å °-0.0397 Å °0.079 Å °0.0357 Å °0.0008 Å °
Refinement TLS groupSelection details: all

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