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- PDB-6v1k: Crystal structure of the first bromodomain (BD1) of human BRD4 bo... -

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Basic information

Entry
Database: PDB / ID: 6v1k
TitleCrystal structure of the first bromodomain (BD1) of human BRD4 bound to BI7273
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-5SW / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 20, 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)15,7637
Polymers15,0991
Non-polymers6646
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.510, 46.590, 78.810
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-5SW / 4-[4-[(dimethylamino)methyl]-3,5-dimethoxy-phenyl]-2-methyl-2,7-naphthyridin-1-one


Mass: 353.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N3O3 / 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.: 99 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
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: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→39.405 Å / Num. obs: 14507 / % possible obs: 100 % / Redundancy: 7.172 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.07 / Χ2: 0.956 / Net I/σ(I): 22.57 / Num. measured all: 104045
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
1.75-1.87.2280.3485.767741107010710.9490.375100
1.8-1.847.2920.28477365101010100.9680.306100
1.84-1.97.2340.2398.2271629909900.9790.258100
1.9-1.967.2670.1999.871009789770.9860.21499.9
1.96-2.027.2780.15412.4368349399390.990.166100
2.02-2.097.2620.12415.2266599189170.9930.13499.9
2.09-2.177.2730.10617.9563138688680.9940.114100
2.17-2.267.2590.09219.7261568488480.9960.099100
2.26-2.367.2340.08620.9260198328320.9960.093100
2.36-2.477.270.07723.3556857837820.9970.08299.9
2.47-2.617.2440.06825.5554627547540.9980.074100
2.61-2.777.1880.06127.8650827077070.9980.065100
2.77-2.967.1530.05232.7647576656650.9980.056100
2.96-3.27.0860.04636.5144646306300.9990.05100
3.2-3.57.0660.0441.9940915805790.9990.04399.8
3.5-3.917.0040.03548.137335335330.9990.037100
3.91-4.527.0040.0325232854694690.9990.035100
4.52-5.536.8340.02849.3228434164160.9990.03100
5.53-7.836.5940.03243.8521433253250.9990.035100
7.83-39.4055.9030.02451.5311511971950.9990.02699

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Processing

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

3mxf


Resolution: 1.75→39.405 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.18
RfactorNum. reflection% reflection
Rfree0.2139 726 5 %
Rwork0.1756 --
obs0.1775 14507 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.71 Å2 / Biso mean: 17.9805 Å2 / Biso min: 5.4 Å2
Refinement stepCycle: final / Resolution: 1.75→39.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 46 99 1206
Biso mean--22.69 24.73 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061144
X-RAY DIFFRACTIONf_angle_d0.8251549
X-RAY DIFFRACTIONf_chiral_restr0.043159
X-RAY DIFFRACTIONf_plane_restr0.005197
X-RAY DIFFRACTIONf_dihedral_angle_d9.715974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.75-1.88510.23361430.17532708
1.8851-2.07480.27441420.17852704
2.0748-2.3750.22481430.17812718
2.375-2.99210.23971450.18772754
2.9921-39.4050.17391530.16692897
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)
13.8680.76870.11337.18653.25947.6198-0.0336-0.1222-0.08170.27610.1658-0.130.3160.2911-0.11510.0481-0.0033-0.01320.10770.01490.085551.221737.288516.048
20.8136-0.79671.00453.8034-1.39763.7262-0.0689-0.16450.14240.2420.04510.0135-0.6077-0.12270.09380.1692-0.00930.06350.1027-0.0130.102447.191358.342320.3738
32.59482.60951.12593.49873.01017.99810.10620.1530.1027-0.32010.03850.7277-0.9431-0.53-0.07960.22910.0357-0.01420.196-0.00460.220140.058854.91227.3662
41.38450.0475-0.07611.034-0.47931.5823-0.0477-0.001-0.0535-0.0871-0.02780.23630.0075-0.1681-0.01930.04730.0137-0.02010.0743-0.01720.108448.760639.84394.7134
56.0741-3.114-1.47934.76952.30565.1686-0.0956-0.2620.02340.02740.02110.42390.109-0.54010.01310.0626-0.0039-0.00390.1085-0.00660.092744.286649.473114.9233
60.6536-1.1655-0.85382.77553.21055.84770.0659-0.0159-0.0087-0.0827-0.0011-0.0802-0.26890.0733-0.08470.0715-0.0266-0.00340.06840.00660.070952.988251.866510.9644
72.95373.1791-0.34226.0921-1.94181.503-0.17441.1113-0.2017-1.36680.0383-0.32860.67510.68570.1160.290.03180.02470.28630.00920.137754.055742.4151-7.5771
82.95770.62660.32054.68191.39922.39250.36150.10790.10670.2041-0.06280.1333-0.41380.0668-0.13190.25160.00290.0380.11530.01690.109247.667755.4855-0.7386
90.92440.2530.51942.8458-0.39830.3983-0.1034-0.20280.09650.6635-0.03680.152-0.0364-0.02670.00010.6191-0.00410.06570.12750.00210.185647.898469.130415.7458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 42 through 51 )A42 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 68 )A52 - 68
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 75 )A69 - 75
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 106 )A76 - 106
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 115 )A107 - 115
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 139 )A116 - 139
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 144 )A140 - 144
8X-RAY DIFFRACTION8chain 'A' and (resid 145 through 163 )A145 - 163
9X-RAY DIFFRACTION9chain 'A' and (resid 164 through 168 )A164 - 168

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