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- PDB-7rjq: Crystal structure of human Bromodomain containing protein 4 (BRD4... -

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Basic information

Entry
Database: PDB / ID: 7rjq
TitleCrystal structure of human Bromodomain containing protein 4 (BRD4) in complex with ILF3
Components
  • Bromodomain-containing protein 4
  • Interleukin enhancer-binding factor 3
KeywordsSIGNALING PROTEIN / Brd4 / ILF3 / acetyllysine
Function / homology
Function and homology information


Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / precatalytic spliceosome / 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 ...Regulation of CDH11 gene transcription / mRNA 3'-UTR AU-rich region binding / negative regulation of viral genome replication / precatalytic spliceosome / 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 / PKR-mediated signaling / double-stranded RNA binding / p53 binding / virus receptor activity / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / Potential therapeutics for SARS / transcription coactivator activity / single-stranded RNA binding / negative regulation of translation / transcription cis-regulatory region binding / chromatin remodeling / ribonucleoprotein complex / protein phosphorylation / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Interleukin enhancer-binding factor 3 / : / : / DZF C-terminal domain / DZF domain / DZF N-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double-stranded RNA binding motif / Double-stranded RNA binding motif ...Interleukin enhancer-binding factor 3 / : / : / DZF C-terminal domain / DZF domain / DZF N-terminal domain / DZF domain profile. / domain in DSRM or ZnF_C2H2 domain containing proteins / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / 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 / Nucleotidyltransferase superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Interleukin enhancer-binding factor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsFedorov, E. / Islam, K. / Ghosh, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123234 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130752 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM118303 United States
CitationJournal: To Be Published
Title: Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization
Authors: Wagner, S. / Fedorov, E. / Sudhamalla, B. / Jnawali, H.N. / Debiec, R. / Ghosh, A. / Islam, K.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Interleukin enhancer-binding factor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,26611
Polymers15,9822
Non-polymers2839
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-64 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.741, 57.115, 123.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-203-

NA

21A-374-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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 BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: O60885
#2: Protein/peptide Interleukin enhancer-binding factor 3 / Double-stranded RNA-binding protein 76 / DRBP76 / M-phase phosphoprotein 4 / MPP4 / Nuclear factor ...Double-stranded RNA-binding protein 76 / DRBP76 / M-phase phosphoprotein 4 / MPP4 / Nuclear factor associated with dsRNA / NFAR / Nuclear factor of activated T-cells 90 kDa / NF-AT-90 / Translational control protein 80 / TCP80


Mass: 883.088 Da / Num. of mol.: 1 / Fragment: UNP residues 99-106 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q12906

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Non-polymers , 4 types, 91 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.0 M sodium chloride, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2018 / Details: KB MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. obs: 16699 / % possible obs: 98.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Χ2: 0.949 / Net I/σ(I): 8.4 / Num. measured all: 110235
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.756.60.9247900.7520.3881.0040.92399
1.75-1.786.60.7368220.8580.3080.7990.87798.9
1.78-1.826.60.6918250.8530.290.750.90499
1.82-1.856.50.5658120.8950.2380.6140.89799.5
1.85-1.896.60.5158590.9130.2170.560.948100
1.89-1.946.60.398000.9420.1640.4241.02698.6
1.94-1.996.60.3278490.9440.1390.3560.91899.3
1.99-2.046.60.2628070.9570.1110.2850.88898.9
2.04-2.16.60.2198470.9740.0930.2381.0198.8
2.1-2.176.60.1558000.9840.0660.1690.87598.5
2.17-2.246.60.1518310.990.0640.1640.93797.9
2.24-2.336.70.1348070.990.0560.1461.03697.6
2.33-2.446.50.1238460.9890.0510.1331.04399.8
2.44-2.576.60.1278520.9880.0520.1381.12799.1
2.57-2.736.60.1258310.9940.0520.1361.1599
2.73-2.946.60.1198280.9930.0480.1290.97999
2.94-3.246.60.1018550.9910.0410.1091.10598.8
3.24-3.76.60.0518510.9980.0210.0551.1799.1
3.7-4.666.80.0328690.9990.0130.0340.68299.4
4.66-306.50.0289180.9990.0120.030.52697.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.8 Å28.56 Å
Translation4.8 Å28.56 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MXF

3mxf


Resolution: 1.72→23.44 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 784 4.9 %
Rwork0.1788 15203 -
obs0.1809 15987 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.29 Å2 / Biso mean: 24.6383 Å2 / Biso min: 9.42 Å2
Refinement stepCycle: final / Resolution: 1.72→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 12 83 1192
Biso mean--37.2 29.55 -
Num. residues----133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.830.28931040.22312208231284
1.83-1.970.25211230.19012437256094
1.97-2.170.2071400.17532559269998
2.17-2.480.22191460.17592608275498
2.48-3.120.24141380.18792631276999
3.12-23.440.20461330.16862760289399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7450.28461.18971.14930.09513.6435-0.182-0.2714-0.08240.04260.0439-0.1486-0.19180.20790.1390.16110.00970.01880.0801-0.02580.16211.720520.8384-5.8917
25.73182.4697-1.18183.6861-0.61043.8469-0.15430.53330.373-0.23460.1850.1062-0.30520.0506-0.05410.1621-0.0167-0.02270.12740.02680.11854.827318.3099-20.6525
31.9767-0.33190.34713.9375-0.75264.1042-0.02510.1467-0.2172-0.01260.02230.10710.2432-0.22870.02530.1355-0.0280.03720.1193-0.01470.1456-1.719.0322-13.089
47.36750.12943.49042.4825-1.05368.2341-0.0651-0.29790.28570.1856-0.0305-0.1402-0.1870.16680.13090.1517-0.03420.01030.1181-0.01440.138812.786820.0224-4.3763
55.78740.91371.96344.05770.83333.8692-0.05760.2233-0.184-0.1079-0.0755-0.08660.14160.08510.06050.14310.00760.05030.1075-0.00570.16648.5517.33-14.933
66.94071.94952.08654.93660.87774.0979-0.06720.2105-0.1535-0.0010.1281-0.5750.09190.6672-0.0610.13790.0220.05140.2827-0.01590.19116.813211.5932-20.1622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 42:72)A42 - 72
2X-RAY DIFFRACTION2(chain A and resid 73:91)A73 - 91
3X-RAY DIFFRACTION3(chain A and resid 92:108)A92 - 108
4X-RAY DIFFRACTION4(chain A and resid 109:124)A109 - 124
5X-RAY DIFFRACTION5(chain A and resid 125:142)A125 - 142
6X-RAY DIFFRACTION6(chain A and resid 143:166)A143 - 166

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