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- PDB-7l6d: Crystal structure of the second bromodomain (BD2) of human BRD2 b... -

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Basic information

Entry
Database: PDB / ID: 7l6d
TitleCrystal structure of the second bromodomain (BD2) of human BRD2 bound to bromosporine
ComponentsBromodomain-containing protein 2
KeywordsGENE REGULATION / BET / ERK5 / dual BRD-kinase inhibitor
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKarim, M.R. / Bikowitz, M.J. / Chan, A. / 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
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,37211
Polymers13,3751
Non-polymers99710
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.260, 35.560, 47.080
Angle α, β, γ (deg.)90.000, 118.810, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-510-

SO4

21A-510-

SO4

31A-646-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13375.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#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.: 1 / Source method: obtained synthetically / Formula: C17H20N6O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 6.5, 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: 1.5418 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→41.254 Å / Num. obs: 17806 / % possible obs: 98.8 % / Redundancy: 3.79 % / Biso Wilson estimate: 23.254 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.114 / Rrim(I) all: 0.127 / Χ2: 0.842 / Net I/σ(I): 15.8 / Num. measured all: 67481 / Scaling rejects: 306
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
1.55-1.592.8180.5665.813576131112690.8660.68396.8
1.59-1.632.9140.3927.263753131112880.9120.4798.2
1.63-1.683.0290.3138.283750124912380.9390.37399.1
1.68-1.733.1270.2429.93681118911770.9610.28899
1.73-1.793.2390.20610.643806118911750.960.24498.8
1.79-1.853.2910.16611.833696113811230.9760.19698.7
1.85-1.923.3410.15613.493652109910930.9770.18399.5
1.92-23.4510.13315.323641106510550.9740.15699.1
2-2.093.4790.12516.623549102810200.9740.14699.2
2.09-2.193.4840.12117.6733909809730.9790.14199.3
2.19-2.313.5530.11718.5232129119040.980.13799.2
2.31-2.453.6340.12419.332318958890.9650.14499.3
2.45-2.623.7520.12320.4430508208130.9730.14299.1
2.62-2.834.060.11921.3531557837770.9830.13599.2
2.83-3.14.6760.11223.7433347167130.9890.12599.6
3.1-3.476.0740.12628.8739366536480.9930.13799.2
3.47-46.7180.11630.437825735630.9910.12698.3
4-4.96.8680.09730.233934954940.9940.10599.8
4.9-6.936.7510.08729.4425723843810.9940.09499.2
6.93-41.2546.2070.07127.8313222272130.9740.07893.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONI

3oni


Resolution: 1.55→41.254 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 891 5 %
Rwork0.1681 16913 -
obs0.1692 17804 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.84 Å2 / Biso mean: 20.6545 Å2 / Biso min: 9.12 Å2
Refinement stepCycle: final / Resolution: 1.55→41.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 65 98 1073
Biso mean--25.1 28.49 -
Num. residues----110
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.64720.26681450.2072274998
1.6472-1.77430.21431470.183279899
1.7743-1.95290.22281480.1788281599
1.9529-2.23550.21651490.16342819100
2.2355-2.81640.18521490.1762843100
2.8164-41.250.15791530.1547288999
Refinement TLS params.Method: refined / Origin x: -1.0802 Å / Origin y: 1.8216 Å / Origin z: 16.1768 Å
111213212223313233
T0.0824 Å2-0.009 Å20.0322 Å2-0.0939 Å20.025 Å2--0.0951 Å2
L2.6038 °20.2414 °20.9745 °2-1.9021 °20.3053 °2--2.3141 °2
S-0.0365 Å °0.0914 Å °0.0414 Å °-0.0579 Å °-0.004 Å °-0.0264 Å °-0.0606 Å °0.035 Å °0.0327 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA346 - 455
2X-RAY DIFFRACTION1allI1
3X-RAY DIFFRACTION1allQ1 - 107
4X-RAY DIFFRACTION1allE1 - 8
5X-RAY DIFFRACTION1allB1

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