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- PDB-7lb4: Crystal structure of the second bromodomain (BD2) of human BRD3 b... -

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Basic information

Entry
Database: PDB / ID: 7lb4
TitleCrystal structure of the second bromodomain (BD2) of human BRD3 bound to bromosporine
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


lncRNA binding / endodermal cell differentiation / protein localization to chromatin / lysine-acetylated histone binding / molecular condensate scaffold activity / chromatin organization / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromosporine / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 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)27,4244
Polymers26,6152
Non-polymers8092
Water2,360131
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,3071
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7122
Polymers13,3071
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.062, 47.638, 64.728
Angle α, β, γ (deg.)90.000, 107.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain-containing protein 3 / RING3-like protein


Mass: 13307.399 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-BMF / Bromosporine / ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3-b]pyridazin-8-yl)carbamate


Mass: 404.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N6O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 10 % w/v Polyethylene glycol 6,000, 5 % v/v (+/-)-2-Methyl-2,4-pentanediol

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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: Aug 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 15413 / % possible obs: 97.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.048 / Rrim(I) all: 0.092 / Χ2: 1.121 / Net I/σ(I): 8.9 / Num. measured all: 56172
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.20.4416970.8630.280.5240.54893.8
2.03-2.073.40.4017650.8420.2520.4750.59494.1
2.07-2.113.50.3217590.8920.1970.3780.61597.4
2.11-2.153.60.2867510.9270.1730.3350.64995.7
2.15-2.23.70.2727380.9140.1620.3180.63397.5
2.2-2.253.70.277760.9280.1620.3150.67196
2.25-2.313.70.2227640.9520.1330.2590.69898.5
2.31-2.373.70.2067490.9580.1240.2410.77395.9
2.37-2.443.70.1777690.9660.1070.2080.71798.8
2.44-2.523.70.1567750.970.0930.1820.77197
2.52-2.613.70.1477610.9780.0880.1720.78898.7
2.61-2.713.70.1127650.9890.0670.1310.87198.3
2.71-2.843.70.1037790.9910.0620.1210.99498.1
2.84-2.993.70.0947780.9910.0560.1091.07698.5
2.99-3.173.70.087770.9920.0490.0941.24998.9
3.17-3.423.70.0648000.9940.0390.0761.66999.6
3.42-3.763.70.0557770.9940.0330.0642.17599.6
3.76-4.313.70.0488020.9960.0290.0562.03599.8
4.31-5.433.70.0438010.9970.0260.051.88199.6
5.43-1003.40.0438300.9970.0270.0512.67399.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L9L

7l9l


Resolution: 2.004→38.135 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1062 6.9 %
Rwork0.1785 14338 -
obs0.182 15400 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.41 Å2 / Biso mean: 30.5032 Å2 / Biso min: 15.81 Å2
Refinement stepCycle: final / Resolution: 2.004→38.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 56 131 1979
Biso mean--23.24 34.1 -
Num. residues----216
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.004-2.09480.32711310.225169793
2.0948-2.20520.25821290.1992173397
2.2052-2.34340.28871330.1857177997
2.3434-2.52430.24681330.1879179197
2.5243-2.77830.25581300.1993178998
2.7783-3.18010.25151330.2012181499
3.1801-4.00590.18151390.15931847100
4.0059-38.1350.20271340.15851888100
Refinement TLS params.Method: refined / Origin x: -14.669 Å / Origin y: 16.0599 Å / Origin z: -15.3597 Å
111213212223313233
T0.203 Å2-0.0118 Å2-0.0025 Å2-0.1725 Å20.0359 Å2--0.1967 Å2
L0.8638 °2-0.279 °2-0.2796 °2-1.0599 °21.1064 °2--1.944 °2
S-0.0394 Å °0.001 Å °-0.0139 Å °-0.0195 Å °0.0806 Å °0.0053 Å °-0.0619 Å °0.0038 Å °-0.0432 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA309 - 416
2X-RAY DIFFRACTION1allB309 - 416
3X-RAY DIFFRACTION1allI1 - 2
4X-RAY DIFFRACTION1allQ1 - 134

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