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

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Basic information

Entry
Database: PDB / ID: 7laz
TitleCrystal structure of the first bromodomain (BD1) of human BRD3 bound to ERK5-IN-1
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 / molecular condensate scaffold activity / lysine-acetylated histone binding / chromatin organization / chromatin binding / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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
Chem-VYJ / Bromodomain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 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)30,4514
Polymers29,1742
Non-polymers1,2782
Water81145
1
A: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2262
Polymers14,5871
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2262
Polymers14,5871
Non-polymers6391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.903, 81.903, 120.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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-VYJ / 11-cyclopentyl-2-({2-ethoxy-4-[4-(4-methylpiperazin-1-yl)piperidine-1-carbonyl]phenyl}amino)-5-methyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 638.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C36H46N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 4.3 M Sodium chloride

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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: 2.3→50 Å / Num. obs: 18845 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.035 / Rrim(I) all: 0.116 / Χ2: 0.963 / Net I/σ(I): 7.2 / Num. measured all: 204933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3410.30.8059370.8370.2620.8480.56100
2.34-2.3810.80.7399130.8550.2340.7760.551100
2.38-2.4310.90.6749020.8980.2130.7080.579100
2.43-2.48110.6099270.9270.1920.6390.576100
2.48-2.53110.5649140.9410.1770.5910.573100
2.53-2.59110.4769250.950.150.50.562100
2.59-2.66110.3939290.9650.1240.4130.597100
2.66-2.7311.10.3399340.9740.1060.3560.613100
2.73-2.8111.10.3139220.9690.0980.3290.781100
2.81-2.911.10.2419220.9830.0750.2520.761100
2.9-311.10.1879350.9890.0580.1960.748100
3-3.1211.10.169320.9920.050.1680.797100
3.12-3.2611.10.1299380.9950.040.1350.932100
3.26-3.44110.1029410.9970.0320.1071.085100
3.44-3.6511.10.0859380.9970.0270.091.185100
3.65-3.93110.0769460.9980.0240.0791.575100
3.93-4.33110.0649600.9980.020.0671.627100
4.33-4.9510.90.0629610.9990.0190.0651.744100
4.95-6.2410.70.0589900.9980.0180.061.364100
6.24-509.40.04610790.9990.0150.0481.95999.8

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LAY

7lay


Resolution: 2.302→41.71 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 1128 6 %
Rwork0.2004 17661 -
obs0.2028 18789 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.33 Å2 / Biso mean: 42.2691 Å2 / Biso min: 23.18 Å2
Refinement stepCycle: final / Resolution: 2.302→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 94 45 2103
Biso mean--45.1 38.39 -
Num. residues----236
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.302-2.40670.28491390.23122166
2.4067-2.53350.33041360.24762145
2.5335-2.69220.2831390.25712175
2.6922-2.90.29981390.25772171
2.9-3.19180.29541390.24062181
3.1918-3.65340.22951410.20342214
3.6534-4.6020.18111430.152239
4.602-41.710.21461520.17742370
Refinement TLS params.Method: refined / Origin x: 19.4344 Å / Origin y: 3.3541 Å / Origin z: 8.4594 Å
111213212223313233
T0.2713 Å20.0032 Å2-0.0311 Å2-0.2596 Å20.0845 Å2--0.2937 Å2
L1.995 °20.2079 °2-0.5473 °2-0.7925 °2-0.0197 °2--1.7339 °2
S-0.0175 Å °0.086 Å °-0.0069 Å °-0.0018 Å °0.0949 Å °0.0888 Å °-0.009 Å °-0.0586 Å °-0.0784 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA25 - 142
2X-RAY DIFFRACTION1allB25 - 142
3X-RAY DIFFRACTION1allI1 - 2
4X-RAY DIFFRACTION1allQ1 - 45

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