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- PDB-6v1u: Crystal structure of the first bromodomain (BD1) of human BRD4 bo... -

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Basic information

Entry
Database: PDB / ID: 6v1u
TitleCrystal structure of the first bromodomain (BD1) of human BRD4 bound to TP-472
ComponentsBromodomain-containing protein 4
KeywordsGENE REGULATION / Bromosporine / BRD4 / BRD / BET / HUNK1
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-QMG / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsChan, A. / Karim, M.R. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Structural Basis of Inhibitor Selectivity in the BRD7/9 Subfamily of Bromodomains.
Authors: Karim, R.M. / Chan, A. / Zhu, J.Y. / Schonbrunn, E.
History
DepositionNov 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4953
Polymers15,0991
Non-polymers3952
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.500, 44.420, 78.310
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 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O60885
#2: Chemical ChemComp-QMG / 3-(6-acetylpyrrolo[1,2-a]pyrimidin-8-yl)-N-cyclopropyl-4-methylbenzamide


Mass: 333.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 94 / 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: 43.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M (NH4)2SO4, 0.1 M Tris (pH 8.5), and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→33.822 Å / Num. obs: 14182 / % possible obs: 99.6 % / Redundancy: 6.758 % / Biso Wilson estimate: 13.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.079 / Χ2: 1.019 / Net I/σ(I): 25.79 / Num. measured all: 95838
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.73-1.777.1930.29914.397639106210620.9740.324100
1.77-1.827.2010.26515.5670219759750.9760.287100
1.82-1.887.1950.21217.9471819999980.9820.2399.9
1.88-1.937.1410.1919.1966489319310.9890.206100
1.93-27.1730.14621.2366499289270.9930.15899.9
2-2.077.0740.12322.963038968910.9920.13399.4
2.07-2.157.0140.125.4960118628570.9950.10899.4
2.15-2.236.8780.08926.7357988468430.9960.09699.6
2.23-2.336.9070.07827.8455268048000.9970.08499.5
2.33-2.456.7410.07229.0751237617600.9960.07899.9
2.45-2.586.660.06929.1147757237170.9950.07599.2
2.58-2.746.5360.06431.0745827057010.9960.06999.4
2.74-2.926.4280.05531.8442496626610.9970.0699.8
2.92-3.166.2880.05233.6337986076040.9980.05699.5
3.16-3.466.1910.05134.5335415785720.9970.05599
3.46-3.876.0740.0535.7431105155120.9970.05599.4
3.87-4.475.9960.05236.327764664630.9950.05899.4
4.47-5.475.8710.04835.6823604034020.9930.05299.8
5.47-7.745.7610.0535.4218323213180.9960.05599.1
7.74-33.8224.8720.05633.319161931880.9950.06297.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXF

3mxf


Resolution: 1.73→33.822 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1996 710 5.01 %
Rwork0.1699 13470 -
obs0.1714 14180 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.31 Å2 / Biso mean: 16.9958 Å2 / Biso min: 5.2 Å2
Refinement stepCycle: final / Resolution: 1.73→33.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 29 94 1175
Biso mean--18.54 25.16 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061113
X-RAY DIFFRACTIONf_angle_d0.7951515
X-RAY DIFFRACTIONf_chiral_restr0.046158
X-RAY DIFFRACTIONf_plane_restr0.005194
X-RAY DIFFRACTIONf_dihedral_angle_d13.602682
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.73-1.86360.18911400.1542648100
1.8636-2.05110.21351390.16212643100
2.0511-2.34780.20521410.16862672100
2.3478-2.95780.21931410.18422692100
2.9578-33.8220.18511490.1693281599
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)
13.8339-0.69571.07451.0836-0.99750.97210.46920.5347-0.46690.28480.2035-0.16291.23680.6224-0.54450.32410.0564-0.04850.1623-0.02030.196615.8061-15.145111.0455
20.90831.0188-0.13672.67232.97816.51640.1259-0.1043-0.03610.3327-0.2893-0.29410.1482-0.11680.13910.1491-0.0238-0.02830.12840.02350.128412.88263.975523.8596
31.34890.01181.18043.17930.92014.4205-0.0458-0.18070.11330.0948-0.03840.3185-0.2324-0.40490.0960.09690.03710.00160.12530.00970.11275.101512.376611.3165
43.5088-1.2179-2.9424.93740.18223.54470.0816-0.02420.0961-0.2669-0.03650.2233-0.1686-0.3215-0.05210.08370.0025-0.04110.0938-0.02790.10984.3681.9747-0.5923
52.5879-1.4047-0.80533.86060.75782.1165-0.06990.0736-0.10910.1190.04170.06310.07610.01750.0090.05730.0095-0.00260.06490.00890.05815.543-8.86495.2168
63.28640.83432.50233.33923.05966.81280.2321-0.20730.11680.0491-0.25030.33250.0431-0.70060.10870.07580.02-0.02130.1020.01110.05947.44842.774114.5013
73.63220.10082.11124.27953.00345.9796-0.1465-0.24780.06310.16580.0681-0.109-0.1095-0.41510.01960.09810.0081-0.01270.11140.00010.042812.42968.016121.7205
81.2269-1.6803-2.25685.11023.97096.5124-0.0051-0.06460.02970.05120.065-0.1848-0.16310.0586-0.10330.0527-0.002-0.0110.06090.01540.080517.44284.60466.6576
92.96460.3617-1.08714.2564-5.61567.78950.11381.423-0.1877-1.21660.1596-0.28080.27020.218-0.01890.315-0.0830.0510.4068-0.01640.189718.0705-2.7606-8.2312
102.44120.25470.23094.20981.18122.9371-0.02940.09460.1225-0.26660.1043-0.0913-0.4219-0.0393-0.04380.0832-0.0027-0.00950.06170.03270.089511.270912.18691.9983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 46 )A42 - 46
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 60 )A47 - 60
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 75 )A61 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 83 )A76 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 106 )A84 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 115 )A107 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 121 )A116 - 121
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 139 )A122 - 139
9X-RAY DIFFRACTION9chain 'A' and (resid 140 through 144 )A140 - 144
10X-RAY DIFFRACTION10chain 'A' and (resid 145 through 167 )A145 - 167

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