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- PDB-7l9l: Crystal structure of the second bromodomain (BD2) of human BRD3 b... -

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Basic information

Entry
Database: PDB / ID: 7l9l
TitleCrystal structure of the second bromodomain (BD2) of human BRD3 bound to BI2536
ComponentsBromodomain-containing protein 3
KeywordsGENE REGULATION / BET / ERK5 / dual BRD-kinase inhibitor
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-R78 / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 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 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8913
Polymers13,3071
Non-polymers5842
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.190, 63.470, 40.000
Angle α, β, γ (deg.)90.000, 109.550, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 13307.399 Da / Num. of mol.: 1
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-R78 / 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide


Mass: 521.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H39N7O3 / 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.: 211 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 293 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 1.5417
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.55→37.694 Å / Num. obs: 18648 / % possible obs: 98.5 % / Redundancy: 2.117 % / Biso Wilson estimate: 11.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.018 / Rrim(I) all: 0.022 / Χ2: 0.999 / Net I/σ(I): 31.39 / Num. measured all: 39475 / Scaling rejects: 2
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
1.55-1.591.3340.04310.71745134913080.9940.0697
1.59-1.631.4190.03912.831940138213670.9950.05598.9
1.63-1.681.5360.0315.472020132913150.9970.04398.9
1.68-1.731.5990.03116.462036128412730.9970.04499.1
1.73-1.791.6650.02918.812035123012220.9970.04199.3
1.79-1.851.720.02621.642028120811790.9980.03697.6
1.85-1.921.7620.02324.072040117211580.9980.03298.8
1.92-21.7880.02126.782006113711220.9980.0398.7
2-2.091.8190.01929.291886105310370.9990.02698.5
2.09-2.191.9010.01833.881922102710110.9990.02598.4
2.19-2.311.9820.01735.6818879749520.9990.02397.7
2.31-2.452.1280.01838.9619519389170.9990.02497.8
2.45-2.622.4940.01945.121378708570.9990.02498.5
2.62-2.833.1440.01951.3325728288180.9990.02398.8
2.83-3.13.6550.01758.5826617327280.9990.0299.5
3.1-3.473.6660.01760.924566766700.9990.0299.1
3.47-43.6610.01762.7822226146070.9990.0298.9
4-4.93.6590.01763.8218155014960.9990.0299
4.9-6.933.5450.01962.4914114033980.9990.02298.8
6.93-37.6943.310.0261.47052262130.9990.02594.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L72

7l72


Resolution: 1.55→37.694 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1777 931 4.99 %
Rwork0.1498 17715 -
obs0.1512 18646 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.82 Å2 / Biso mean: 15.5505 Å2 / Biso min: 4.89 Å2
Refinement stepCycle: final / Resolution: 1.55→37.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms931 0 42 211 1184
Biso mean--20.13 25.39 -
Num. residues----113
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.63170.17281310.1448248098
1.6317-1.73390.18881340.1467254899
1.7339-1.86780.20191320.1611250699
1.8678-2.05570.19231320.1541252399
2.0557-2.35320.16861340.1519253398
2.3532-2.96450.18411330.1555253999
2.9645-37.690.16491350.1425258699

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