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- PDB-7l9g: Crystal structure of the second bromodomain (BD2) of human BRD2 b... -

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Basic information

Entry
Database: PDB / ID: 7l9g
TitleCrystal structure of the second bromodomain (BD2) of human BRD2 bound to BI2536
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / BET / ERK5 / dual BRD-kinase inhibitor / GENE REGULATION / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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 phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
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-R78 / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 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)14,0575
Polymers13,3751
Non-polymers6814
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.530, 71.550, 32.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-504-

CL

21A-783-

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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25 % w/v Polyethylene glycol 3350

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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: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.36→35.775 Å / Num. obs: 24096 / % possible obs: 90 % / Redundancy: 3.48 % / Biso Wilson estimate: 11.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Rrim(I) all: 0.025 / Χ2: 1.005 / Net I/σ(I): 32.15 / Num. measured all: 83854 / Scaling rejects: 3
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
1.36-1.41.9590.1484.712118196210810.9520.19355.1
1.4-1.432.4260.1157.263297190413590.970.14571.4
1.43-1.482.6550.0929.133876183014600.9860.11479.8
1.48-1.522.8430.0811.634315178815180.990.09884.9
1.52-1.572.9710.06414.624585173715430.9940.07888.8
1.57-1.633.0720.05517.594863171015830.9960.06692.6
1.63-1.693.1610.04720.664861162715380.9970.05794.5
1.69-1.763.2280.04223.334820155814930.9980.0595.8
1.76-1.833.2970.03627.034817151014610.9980.04296.8
1.83-1.923.3470.03132.24853146614500.9990.03798.9
1.92-2.033.3980.02638.064587136913500.9990.03198.6
2.03-2.153.4220.02541.84497132413140.9990.02999.2
2.15-2.33.4550.02346.184225123412230.9990.02799.1
2.3-2.483.5530.02148.764065115111440.9990.02599.4
2.48-2.723.7620.02152.43976105910570.9990.02499.8
2.72-3.044.2820.0259.5741499769690.9990.02399.3
3.04-3.515.9340.0272.16509786485910.02299.4
3.51-4.36.7070.01980.33499774774510.0299.7
4.3-6.086.4130.01877.738486016000.9990.0299.8
6.08-35.7755.7540.0273.1200835934910.02297.2

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Processing

Software
NameVersionClassification
PHENIX1.19_4085refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONI

3oni


Resolution: 1.36→35.77 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1722 1085 4.5 %
Rwork0.149 23008 -
obs0.1501 24093 89.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.21 Å2 / Biso mean: 17.2205 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: final / Resolution: 1.36→35.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 98 209 1217
Biso mean--25.16 29.11 -
Num. residues----110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009983
X-RAY DIFFRACTIONf_angle_d1.4991324
X-RAY DIFFRACTIONf_dihedral_angle_d14.155136
X-RAY DIFFRACTIONf_chiral_restr0.079131
X-RAY DIFFRACTIONf_plane_restr0.008167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.36-1.420.2512910.23131926201761
1.42-1.50.20531170.16252494261180
1.5-1.590.18341330.14922804293789
1.59-1.710.17641400.15152984312494
1.71-1.890.18181450.14563083322897
1.89-2.160.14281490.14143146329599
2.16-2.720.17171510.13693209336099
2.72-35.770.17011590.15183362352199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8293-1.46111.90692.373-2.06223.7051-0.0749-0.020.10320.01690.0366-0.0535-0.20810.10580.06580.0846-0.04430.00670.0888-0.01380.07739.743611.38032.5035
21.228-1.4621-0.55154.6421-0.58650.85940.01070.0137-0.0363-0.1249-0.0267-0.15090.08350.17480.01750.06070.02520.00380.10920.00320.074518.5643-7.51130.4239
34.267-0.28822.12843.9313-2.55118.40430.04160.21490.063-0.2428-0.1051-0.121-0.13510.29870.04860.1115-0.00850.02290.0862-0.01690.069512.48098.2099-9.2926
41.239-0.5001-0.29872.0751-0.30351.617-0.0076-0.03760.0360.04050.0590.0431-0.0050.0375-0.05230.0371-0.0149-0.00040.049-0.00930.06895.34621.20573.8721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 346 through 372 )A346 - 372
2X-RAY DIFFRACTION2chain 'A' and (resid 373 through 395 )A373 - 395
3X-RAY DIFFRACTION3chain 'A' and (resid 396 through 410 )A396 - 410
4X-RAY DIFFRACTION4chain 'A' and (resid 411 through 455 )A411 - 455

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