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- PDB-7lay: Crystal structure of the first bromodomain (BD1) of human BRD3 bo... -

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Basic information

Entry
Database: PDB / ID: 7lay
TitleCrystal structure of the first bromodomain (BD1) of human BRD3 bound to SG3-179
ComponentsBromodomain-containing protein 3
KeywordsGENE REGULATION/INHIBITOR / BET / ERK5 / dual BRD-kinase inhibitor / GENE REGULATION / GENE REGULATION-INHIBITOR complex
Function / homology
Function and homology information


histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding ...histone H3K27cr reader activity / histone H3K18cr reader activity / histone H3K9cr reader activity / histone H3K9me2/3 reader activity / lncRNA binding / endodermal cell differentiation / protein localization to chromatin / : / molecular condensate scaffold activity / histone binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-5W2 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKarim, M.R. / Bikowitz, M.J. / Schonbrunn, E.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.
Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E.
History
DepositionJan 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 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 3
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6007
Polymers29,1742
Non-polymers1,4275
Water4,143230
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2533
Polymers14,5871
Non-polymers6662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3474
Polymers14,5871
Non-polymers7603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.007, 61.643, 93.732
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 3 / RING3-like protein


Mass: 14586.843 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q15059
#2: Chemical ChemComp-5W2 / 4-[[4-[[3-(~{tert}-butylsulfonylamino)-4-chloranyl-phenyl]amino]-5-methyl-pyrimidin-2-yl]amino]-2-fluoranyl-~{N}-(1-methylpiperidin-4-yl)benzamide


Mass: 604.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H35ClFN7O3S / 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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3,350

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→100 Å / Num. obs: 49274 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.54 Å2 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.045 / Rrim(I) all: 0.107 / Χ2: 6.715 / Net I/σ(I): 20.5 / Num. measured all: 185069
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.482.60.35422580.8210.2680.4470.48892.2
1.48-1.52.70.30523210.8540.2280.3830.51892.8
1.5-1.532.70.27623130.870.2030.3450.59194.8
1.53-1.562.80.24223680.9070.1750.30.6295.3
1.56-1.62.80.2123850.9280.150.260.65796.6
1.6-1.632.90.17723820.950.1230.2170.74497.1
1.63-1.6730.16624570.9540.1130.2020.81698
1.67-1.7230.14624530.9670.0990.1770.85199.1
1.72-1.773.10.13224630.9720.0870.1580.99299.9
1.77-1.833.20.11424780.980.0740.1371.102100
1.83-1.893.30.124790.9820.0640.1191.341100
1.89-1.973.40.08525100.9880.0530.1011.587100
1.97-2.063.40.07424910.990.0460.0881.908100
2.06-2.173.90.12525010.9750.0660.14212.075100
2.17-2.34.10.12625160.9690.0660.14314.6100
2.3-2.484.30.12225090.9770.0610.13713.494100
2.48-2.734.60.11725310.9790.0570.1313.647100
2.73-3.125.10.11825580.980.0550.1313.357100
3.12-3.946.60.11425830.9890.0480.12413.568100
3.94-1006.70.05627180.9940.0230.0614.50799.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NXB

3nxb


Resolution: 1.45→42.729 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 1231 2.5 %
Rwork0.1659 47977 -
obs0.1664 49208 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.48 Å2 / Biso mean: 18.2637 Å2 / Biso min: 9.75 Å2
Refinement stepCycle: final / Resolution: 1.45→42.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 94 230 2268
Biso mean--22.49 26.51 -
Num. residues----233
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4501-1.50820.23041270.2015496193
1.5082-1.57680.19711300.1838506795
1.5768-1.65990.19811350.1638523697
1.6599-1.76390.20591360.1609533399
1.7639-1.90010.19691380.15975360100
1.9001-2.09130.15091380.16255407100
2.0913-2.39390.19871400.16595445100
2.3939-3.0160.22111400.17615478100
3.016-42.720.16611470.15835690100
Refinement TLS params.Method: refined / Origin x: -23.6044 Å / Origin y: 7.0484 Å / Origin z: -13.0226 Å
111213212223313233
T0.1226 Å2-0.0045 Å2-0.0039 Å2-0.129 Å2-0.0016 Å2--0.1058 Å2
L0.6127 °20.1061 °2-0.1562 °2-0.6372 °20.003 °2--0.468 °2
S-0.0121 Å °-0.0071 Å °-0.0011 Å °0.0253 Å °0.0069 Å °-0.0214 Å °0 Å °0.01 Å °0.0054 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA22 - 142
2X-RAY DIFFRACTION1allB33 - 144
3X-RAY DIFFRACTION1allI1 - 2
4X-RAY DIFFRACTION1allQ1 - 234
5X-RAY DIFFRACTION1allC1 - 2
6X-RAY DIFFRACTION1allD1

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